Kal-El of former Earth-Prime is the most powerful kryptonian in the DC Multiverse, except for the Kal-El (DC One Million) of the 853rd Century, and has no practical limitations in his ability to directly use or overwhelm other physical or energy sources for his own.
Due to his existence out of Multiverse, because of the death of his home world in Crisis on Infinite Earths, he is completely immune to the reality-changing abilities of his enemies (such as imps of Fifth Dimension).
At present in the alternate recreation of Earth-Prime he currently inhabits, Prime restored all of his previous powers due to actions by Black Lantern Alexander Luthor.
While he was formerly empowered by the energies of the Guardians of the Universe, Prime showed he was able to enter into the Fifth Dimension at will as well as the Source Wall itself. These Oan energies aged him to adulthood, increasing his powers even more than normal, thought they wouldn't last, as he used them all up to fight against Monarch. Since that battle Prime has reverted to his former physical age and his powers have returned to his pre-Countdown power levels.
In at least one possible timeline, Prime will become the Time Trapper and have literally access to all powers and abilities from across all time.
Prime's cellular structure is more dense, resilient and biologically more effective than human tissue. Strangely enough, he does not seem to possess superhuman strength levels despite his enhanced cellular ability without constant exposure to yellow solar energy. Without such charging, his strength seems on par for a human of his height and weight who engages in regular physical activity. As an alien he possess several organs whose functions are not yet disclosed or understood but are believed to be part of and perhaps even the source of his biomatrix force field and reclamation aura. Prime's body also stores energy actively within his bio-cellular matrix as an energy pattern that is linked to his body's electromagnetic field. This energy powers most of Prime's electromagnetic capabilities such as flight and heat vision. It also supplements his physical strength by a factor of 12,000 times or so.
Technically, this is the primary source of Prime's powers. Because Prime's powers are mostly the result of his ability to absorb and process yellow sun energy, his powers have been affected by extreme absorptions of solar power, whether voluntary or involuntary. Prime seems either unique due to his hailing from another dimension or maybe this may be an unknown advancement of this ability that other Kryptonians have yet to achieve. Prime's body is not limited to processing only yellow sun energy as the energy of the willpower-manipulating energy of the Guardians is completely compatible to his body's energy processing ability. It is unclear what other energy sources Prime's cells can effectively process. But presently only these two separate and distinct known sources (yellow solar energy and Guardian mental energy) are the most effective.
Prime has near infinite physical strength under his own original superhuman levels, which are present in all of his other physical abilities as long as he is charged by yellow solar radiation. Fully charged, Prime has repeatedly shown himself to be able to move entire planets out of their orbits at will and has defeated multiple attacks by fully charged other dimensional Kryptonian counterparts to himself at his regular "charged-up" levels. He is strong enough to kill powerful enemies by accident like he did with Wildebeest and Pantha.
Fully charged in a yellow star solar system, Prime is impervious to all known physical attacks and has directly survived traveling through a sun. He is so invulnerable that he could survive going through a red sun which makes him lose his powers with no injuries.
Prime has the ability to maintain continuous strenuous physical action for an undefined period. Theoretically, most incarnations of the character has unlimited stamina as his enhanced nourishment is produced from the solar energy his cells process; however his base physical structure still does need to process food stuffs as well as has the psychological need to eat and drink just as Earth humans do, despite the fact that his superhuman powers receives the majority of that power from a yellow sun.
Through an act of will, Prime can fly without the aid of wings or other navigational devices. His recorded speed while flying under yellow solar energy only has been noted to be well beyond light speed being able to do independent time travel by exceeding the light speed barrier as evident during the Infinite Crisis saga, rather than the slower vibrational matching technique that Barry Allen, Bart Allen and Jay Garrick use to move in time.
Prime possesses the ability to move at an incredible speed. While not nearly as fast as the Flash, he is able to exceed light speed. This includes running at speeds that are beyond supersonic, but usually engages in flying as that is usually less strenuous and more versatile. As stated above, his flight speed is beyond light speed and is able to time travel to an extent exceeding the light speed barrier.
Prime can generate a concentrated gust of wind from his mouth capable of freezing matter within a limited range, as evidenced by him freezing several Green Lanterns to death while fighting them off in space and even freezing Red Star after he had powered up.
Enhanced Senses: Prime possesses super enhanced senses that allow him to detect vibrational movements at least in the sub-atomic motion level. Some of his known super-senses include
Vision specific powers
Prime can perceive objects at great distances. The range of his telescopic vision is unknown, but he can see objects from several hundred miles away. This ability operates independently of normal vision and can be activated or deactivated by an act of will.
Through an act of will, Prime can perceive items in the electromagnetic spectrum. He can see through solid objects of varying depths and thickness. The exact range of Prime's X-ray vision is unknown.
The ability to see extremely small objects and images down to the atomic level (normal optical microscopes can only see objects down to the size of chromosomes).
Infrared Vision Prime can see in total darkness
Electro-magnetic Spectrum Vision
can see well into most of the EM Spectrum. He can see and identify radio/television and any and all broadcast/transmitted frequencies, allowing him to avoid detection through radar or satellite monitoring methods.
Prime can generate beams of intensified heat from both of his eyes. His heat vision is strong enough to melt through Titanium steel and other durable metals. His heat vision also generates concussive force, which can repel opponents away from him and injure opponents like some of the Green Lanterns he fought, even though they were protected by their ring's energy or Bushido who was sliced in half. He can also control the size of the beams and change their strength.
Other super-sensory powers
Prime has the ability to hear any sound at any volume or pitch from vast distances. This power is suggested to be a form of mental telepathy that corresponds to sound as he has been shown to hear sounds in outer space where there is no air for the sounds to travel through.
Prime has a high resistance to magical based attacks as he was only minimally effect from a blast from Black Adam, stating that it only "tickled" him. As the same effect happened when he was attacked by Mordru.
Power Mimicry Immunity
Prime possessed an ability to nullify the effects of others trying to duplicate his powers. This was shown when fighting Amazo replying that "trying to copy my powers.....wrong!!!!"
Krypton of Earth-Prime's universe�unlike other versions of the planet�was swallowed up by its sun Rao, rather than destroyed in an explosion that might have created Kryptonite, so there is no known Kryptonite that can affect Prime. Prime, as well as Superman of Earth-Two, has been shown to be immune to the Kryptonite of the New Earth Universe. Presently, there is no known existing variant of Kryptonite that originates in the current reality that can effect Prime.
It is unknown if Kryptonite from any of the other known 52 universes or antimatter universes can effect him.
An artificial variant was created in the Legion of Super-Heroes' time that had an effect on Prime. It is unknown at this time if it would kill Prime or merely irritate him as shown.