The team came from a goal down after midfielder Mohamed Elneny had put Egypt ahead midway through the first half.
Nicolas Nkoulou scored the equalizer 60 minutes in the game, when Egypts’ energy seemed to diminish. Cameroon added a gear, creating chances befor Aboubakar struck the winner in the 88th minute after chesting the ball down, over defender Ali Gabr.
The victory means that Cameroon won its first title since 2002, denying Egypt a triumphant return to the tournament they last won seven years ago.
“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.
Broos had to deal with a host of refusals from key players to accept call-ups for the Cup of Nations but a new squad defied expectations to reach the final, where they beat Egypt 2-1 in Libreville.
"It's true that when I came to Cameroon nearly a year ago I found a group of players who were old, not motivated, so I had to change that," Broos said after the Indomitable Lions came from behind to beat Egypt with goals from Nicolas Nkoulou and Vincent Aboubakar.
"The players were not coming to play for Cameroon, they were going because they had to, because the coach asked them to come.
"So I brought in some new young players and we started working. We did a good job and now today we have a team.
"We are still not on the highest level. We need to be much better, but it's already a great beginning.
"I am very happy that we won the Cup of Nations today and I am happy for the players -- this is not a group of football players, they are a group of friends."
Broos added that he needed to have some strong words for his players at the interval after a first half in which Egypt were on top.
The Egyptians led through a Mohamed Elneny goal midway through the first half but Nkoulou levelled just before the hour and Aboubakar won it with two minutes left.
"I think in the first half we were tactically not in good positions. The midfield was dominated by Egypt and we had some positional mistakes," Broos said.
"It's very difficult to change that during the game so at half-time I told them what they had to do and they did what I asked of them.
"You see the result. But it's not only that -- we were physically much better than Egypt."