As a genin, Obito's abilities were average at best, struggling to match his classmates from the Academy. Determined to improve himself, he trained for several months at a time to eventually become a chūnin. Madara saw great potential in Obito and thus selected him as his disciple. Madara's hopes were proven correct, as under his tutelage, Obito dramatically improved his abilities as a late bloomer, with his skills leading to others questioning if he was Madara. As a teenager Obito posed a threat to the Five Great Shinobi Countries, having taken control of the Fourth Mizukage and effectively Kirigakure, as well as posing a challenge to the Fourth Hokage and nearly destroying Konoha. As an adult, he defeated Root's most skilled ninja, and simultaneously held his own against Konoha's top shinobi and Killer B. As the Ten-Tails Jinchūriki, Obito's power exceeded that of even Hashirama Senju, he was able to effortlessly fight three powerful Hokage with ease, overwhelm both Naruto and Sasuke several times, and had the capability to destroy the entire Allied Shinobi Forces.

Obito's chakra reserves were enhanced by the White Zetsu matter equipped to his body, enabling him to perform several chakra-taxing techniques without noticeable exhaustion. He showed the ability to absorb chakra, as well as transfer his own to another person. Obito was proficient in taijutsu as he fought on par with Kakashi on several occasions, while controlling the outcome of their last fight. His physical strength and speed were great enough to lift Konan by her throat with one hand while gravely injured,[ and keep up with Naruto's Nine-Tails Chakra Mode.

The right side of Obito's body was badly damaged during the mission in Kusagakure, and he even lost his right arm. To heal his body and replace the limb, Madara outfitted Obito with the same substance that the White Zetsu are made of, enhancing his chakra reserves and eventually allowing him to perform Wood Release. He also gains certain physical augmentations of Hashirama Senju's DNA, such as great durability to attacks, rapid healing, and the ability to survive without food or water. His artificial limb is very strong, able to withstand an attack from Kubikiribōchō and punch through boulders. If this or another limb is damaged beyond repair, they are easily removed and replaced with the same material.

Obito learned from Madara how to perform a variety of different types of ninjutsu: he could create barrier ninjutsu, using the Uchiha Flame Formation to protect the Demonic Statue; he could sense chakra, allowing him to predict attacks and locate others from great distances, even in different dimensions and he could perform fūinjutsu powerful enough to seal the Ten-Tails

Obito could utilise all five basic nature transformations along with Yin–Yang Release. As an Uchiha, he had a natural aptitude for Fire Release techniques, and could perform the Great Fireball Technique at an early age. The size and strength of his flames increased in his adulthood, and through a combination with his Mangekyō Sharingan he could perform Fire Release: Blast Wave Wild Dance. He was also seen performing Earth Release techniques on occasion, though he exclusively did so in order to burrow and move underground, letting him augment the battlefield from below or sneak up on opponents.

With the White Zetsu matter used as his replacement limbs, Obito could perform Wood Release, a combination of earth and water-based chakra. Instinctively, he was able to form branches and roots to bind, crush, or skewer opponents. Because the White Zetsu material is partly derived from the DNA of Hashirama Senju, Obito could control the Ten-Tails when he was connected to its body.

Like many Uchiha, Obito was trained in shurikenjutsu, allowing him to throw shuriken with precision for offence and defence. When Madara died, a number of weapons were left to Obito which he has used at different times over the years. Several of these weapons he keeps stored within Kamui's dimension so that he can access them anywhere and fire them at opponents; he is seen using giant shuriken and chakra receivers – fashioned into giant restraining stakes – for the latter purpose. When he fought Minato during the attack on Konoha, he used a long chain attached to braces on his wrists that, when used in conjunction with his intangibility, enabled him to harmlessly pass through his opponent before solidifying to restrain him with the trailing chain. Around the time of the Uchiha Massacre, Obito carried a sword at his waist. During the Fourth Shinobi World War he wields Madara's iconic gunbai, using it both as a shield and as a sort of flail for attack. The gunbai can generate wind to reflect attacks.

When Obito first awakened his Sharingan, it already had two tomoe, which at that level he could use to track chakra signatures and predict movements. He acquired a third tomoe after witnessing Rin's death. Obito keeps his Sharingan active seemingly all the time without any noticeable drain on his chakra levels. With his Sharingan he can perform various genjutsu on targets he has eye contact with, either to create illusions, acquire information, or control their actions. Although he is seen controlling six tailed beasts with his Sharingan, his control with multiple targets is not as complete as it is with one and it is possible for some to break free from his control.

Obito has a number of Sharingan in his possession which he keeps in storage should he need them. He uses one of these Sharingan to replace the one he gave to Kakashi, although he keeps it covered with his mask most of the time. He later sacrifices this spare eye's vision in order to perform Izanagi, which allows the user to manipulate events around them. Izanagi ordinarily lasts for only the briefest of moments, but with his access to Hashirama's DNA he can maintain it for ten minutes using a single eye.

Obito awakened his Mangekyō Sharingan after witnessing Rin's death; the Sharingan he gave to Kakashi awakened its Mangekyō at the same time. Their Mangekyō's design is three stretched triangles evenly spaced around the pupil that each curve at the top around the eye to form a circle, making it similar to a pinwheel. Obito does not appear to suffer any adverse effects from using his Mangekyō Sharingan, such as the deteriorating eyesight or exhaustion experienced by others.

Obito's Mangekyō Sharingan allows him to perform Kamui, a space–time ninjutsu with greater versatility than Minato's. Kamui serves as a gateway to another dimensional space, which he can move all or parts of his body between at will. This grants Obito two distinct abilities: teleportation and what is best described as "intangibility". For teleportation, he absorbs himself through his right eye into the special dimension, and from there he can travel anywhere in the world instantly. His intangibility is a more specialised application of the teleportation, where he sends only parts of his body to the other dimension so that he can pass through objects or, more often, objects can pass through him. He can only make himself continuously intangible for about five minutes at a time before needing to rest.

Kamui becomes Obito's signature fighting style to the point that he rarely resorts to more traditional forms of ninjutsu. In combat he uses his intangibility defensively, allowing opponents and their attacks to pass through him without harming him, and then as offence he teleports them to his dimension while they are disoriented so that they can no longer bother him. The chakra signatures of those he sends to the other dimension cannot be sensed from outside of it. Despite how useful Kamui is, it isn't without its weaknesses. Because the two aspects of the technique are connected he can't use both at the same time; if he wants to teleport he can't be intangible, leaving him open to attack, and if he wants to be intangible he can't teleport, preventing him from escaping so long as he remains on the defensive.

Because Kakashi's Mangekyō Sharingan can also use Kamui, his eye remains the only reliable counter to Obito's abilities. Although Kakashi cannot use Kamui against Obito directly, he can use his own access to the other dimension to negate the advantages Obito makes use of: by teleporting attacks or allies to the other dimension at the same moment that Obito's body resides there for defence, he can be attacked successfully. He regains the Sharingan he gave to Kakashi during the Fourth Shinobi World War, allowing him to use the eye to perform rapid, precise long-distance teleportation instead of the physical contact required with his other eye's teleportation. With effort, he can use his left Mangekyō to access other dimensional planes.

Obito took the Rinnegan from Nagato's body after he died and implanted it in his left eye socket. Although he used only one eye and was not its original owner, Obito nevertheless gained a great deal of power from it. While he admitted that he could barely handle a single eye, Obito was capable of performing all of the Six Paths Techniques with the Rinnegan, though he was only ever seen performing abilities of the Outer Path: he can summon the Demonic Statue of the Outer Path, create chakra chains to restrain targets, and use the Samsara of Heavenly Life Technique to revive the dead in exchange for his life.

While in possession of the Rinnegan, Obito used it to create his version of the Six Paths of Pain, composed of the six reincarnated jinchūriki with their respective tailed beasts sealed back into their bodies. He controls them each with a single chakra receiver embedded into their bodies. Each jinchūriki had the same eye-pattern as him – a right Sharingan (which granted them its predictive abilities) and a left Rinnegan – allowing him to share their vision and coordinate their movements. The effort required to not only maintain this coordination but to keep the tailed beasts under his control prevents Obito from manifesting any of the Six Paths Techniques in his Six Paths of Pain.

Obito seals the Ten-Tails into his body during the Fourth Shinobi World War. Upon becoming its jinchūriki, all of the previous damage to his body is healed and he becomes stronger, faster, and nearly impervious to damage. He initially lacks control of his mind after the sealing, causing him to literally swell with the Ten-Tails' chakra and react relentlessly to all threats until he can pull himself together. Once he does, Obito becomes stronger than the original Ten-Tails because he is able to focus its immeasurable power, leaving so-called God of Shinobi unable to compete with him. As the Ten-Tails' jinchūriki, Obito can fly and create chakra arms. He can produce trees through which he can fire Tailed Beast Balls, and later create and control the Ten-Tails' tree form in preparation for performing the Infinite Tsukuyomi. He is unable to use Kamui's intangibility while a jinchūriki, however.

As the Ten-Tails' jinchūriki, Obito is able to use Truth-Seeking Balls, ten black orbs comprised of all five elemental nature transformations, and Yin–Yang Release. The balls are his primary weapons and generally float behind him in a halo-like formation. The black chakra is highly malleable, able to be shaped into various forms for different uses, such as high speed projectiles, protective barriers, explosives, and various weapons, including a shakujō reminiscent of the Sage of the Six Paths'. He can even recreate the Sage's Sword of Nunoboko, with which Obito claims he can lay waste to the world. With his complete control over the Ten-Tails' power, Obito can apply Yin–Yang Release to nullify all ninjutsu the balls come in contact with. Unique to Obito, he is able to increase the size of his Truth-Seeking Ball by passing them through holes in his hand.