Cameroon, who had eight of their players withdraw before the tournament, came from a goal down after midfielder Mohamed Elneny had put Egypt ahead midway through the first half.
Nicolas Nkoulou equalised on the hour and, as Egypt tired, Cameroon appeared to find a new gear, creating several chances before Aboubakar struck the winner in the 88th minute after chesting the ball down and flicking it over defender Ali Gabr.
It was Cameroon's first title since 2002 and denied Egypt a triumphant return to the tournament they last won in 2010, while at the same time inflicting a first loss on the North African side in 25 Nations Cup matches dating back to 2004.
"We are delighted but we are not yet the finished product. We can still make a lot of improvement," said Cameroon's delighted Belgian manager Hugo Broos.
Egypt dominated the early possession and had the lead after 22 minutes as Cameroon’s defence stood far too static.
Elneny collected the ball in space on the right-hand side of the area and, with the defence and goalkeeper Fabrice Ondoa expecting him to square the ball into the six-yard box, the midfielder rifled his shot into the roof of the net.
TACTICAL MASTERSTROKE
Cameroon created few chances in the first half and were reduced to shooting from distance but they upped their intensity in the second period and began to exert some control.
They levelled when substitute Nkoulou towered above the defence to head home a cross from Benjamin Moukandjo, only the second goal conceded by the North Africans in the tournament.
Cameroon then attacked in waves as Egypt appeared to be holding out for extra-time and penalties.
It looked as though the game was headed that way with Cameroon wasting with their opportunities until a moment of excellence from Aboubakar, brought on in what proved a tactical masterstroke by Broos, two minutes from the end.
The striker, who plays his club football in Turkey with Beskitas, controlled the ball on his chest in the box and, as Ali Gabr stood off him, he skilfully knocked it over the defender's head and fired into the far corner of the net.
For Egypt coach Hector Cuper it was more disappointment. Having lost five finals in club football, including Europe's elite Champions League twice, he is an unlucky loser again at international level.
"Cameroon deserved to win. I have deep sorrow for my players but it was too much for them, they were too tired. For myself, losing another final, I don't want to say I'm getting used to it," the Argentine said.
But for Cameroon’s young Indomitable Lions it was a moment of unexpected triumph in a tournament the country will host in two years' time as defending champions.
(This story has been refiled to fix a typo in paragraph 12.)
(Reporting by Mark Gleeson; Editing by Ken Ferris)
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