Security forces opened fire when militants strapped with suicide bombing vests approached aircraft hangars, prompting other militants to fire rocket-propelled grenades from outside the base's walls, said the air force spokesman.
Base commander Air Commodore Muhammad Azam, who led the operation against the attackers, was shot in the shoulder, but is in stable condition, said spokesman Captain Tariq Mahmood.
Search operations for any other militants who may have been hiding in the complex after the attack had ended, he said.
About an hour later, a series of small explosions could be heard as homemade bombs planted on the base by the militants were detonated by the military.
Minhas, 45 miles northwest of Islamabad, is adjacent to the Pakistan Aeronautical Complex, a major air force research and development center. Pakistan manufactures JF-17 fighter planes, jointly developed with China, at the site.
Suicide bombers launched attacks near the base and the aeronautical complex in 2007 and 2009, but news reports said defenses were not breached.
It was not immediately clear how the attackers managed to enter the sprawling base this time. Although the attack took place at about 2 a.m., it is likely many of the soldiers on the base were awake for prayers or breakfast during the holy fasting month of Ramadan.
Faheemullah Khan, a civilian who lives near the base, said he was at a mosque praying when he heard gunfire and explosions which he thought were military exercises.
"Then we came to a restaurant, which is next to the main entrance to the base, and heard a louder explosion," he said.
"We saw six police vans rush in, and realized something was wrong."