The pilot had successfully completed a raid against kidnappers when the plane came under intense enemy fire.
"Using his survival instincts, the pilot, who came under intense ground fire from the bandits, was able to evade them and sought refuge in nearby settlements awaiting sunset," Air force spokesman Edward Gabkwet said in a statement.
The pilot, Abayomi Dairo, found his way to an army base where he was rescued after ejecting from the cockpit, German newswire Deutsche Welle reports.
The attack happened in the north west of the country on the border of the northern Zamfara and Kaduna states.
Armed gangs – who are referred to as "bandits" – are believed to be behind a surge in kidnappings in this part Nigeria.
The kidnappings have targeted schoolchildren, and more than 1000 have been kidnapped since December, the BBC reports.
The kidnappers demand ransoms and in most cases the school children have been freed after it is paid, however some have been killed.
Boko Haram is the most well-known of the militant group battling for control of parts of northern Nigeria and neighbouring countries.
On orders from President Muhammadu Buhari, the military have been mounting day and night operations to "neutralise" the bandits in the north west region.
"Through these intensive air operations, hundreds of bandits have been neutralised and several of their hideouts destroyed," the Nigerian Air Force said in a statement.
There have been several plane crashes this year involving military jets, however this is the first the Nigerian Air Force has attributed to bandits.
In May, the Nigerian Army chief, Lt Gen Ibrahim Attahiru, was killed, along with 10 other officers, in a plane crash.
A month earlier, an Alpha Jet crashed in the state of Borno - one of the areas where Boko Haram militants are most active.
However, the military denied it was the result of terrorist activity.