The match a repeat of the 2008 final which Egypt won. Cameroon Fabrice Ondoa was first to spring into action when he held on to a stinging low drive from Egypt's Abdallah El-Said.
Egypt's 44-year-old goalkeeper Essam el-Hadary saw Aboubakar's tournament-winning shot slip past him, denying el-Hadary an incredible fifth title with Egypt almost 20 years after his first. They said they were too busy with important games for their European teams.
Hosts on several Egyptian television channels looked grim as they reported on the Pharaohs' loss.
On Sunday, Cameroon faced up to those odds once again and having gone a goal down early on, crafty substations (some forced, some chosen) by Broos paid off.
For Broos, much criticised by the Cameroon press since taking over, the result was vindication for his new approach.
"There was a lot of trouble before, players who wouldn't come with us", said the Belgian, reported by the Echo.
The last Cup of Nations final to feature more than a single goal came in 2004, when Tunisia beat Morocco 2-1.
Cameroon were without the services of eight players for the tournament, with Matip the highest-profile absentee after claiming that he has retired from worldwide football, which would also rule him out of several Liverpool games.
Despite a solid record heading into the tournament (they'd lost just once in 2016), Cameroon weren't even considered underdogs, they were no-hopers.
Mohamed Elneny had put Egypt in front midway through the first half but a stirring second-half performance from Cameroon saw Nicolas Nkoulou equalise before Aboubakar fired home with a sublime piece of skill in the 88th minute.
That was Cameroon's last final appearance, but while then they had the likes of Samuel Eto'o and Rigobert Song, their current team has no such big name stars.
The Lyon midfielder rose above the Egypt defence to meet a deep Benjamin Moukandjo cross from the left and head past a helpless El Hadary.
It was evident that the advance had injected loads on confidence into the ranks of Cameroon's Indomitable Lions and in the 67th minute, their pressure earned them a fourth corner in the match.
Then, as the game appeared set for extra time, Aboubakar collected possession, looked up, and made a decision to do it all by himself.
The Lions, who were not favourites, at the start of the competition, demonstrated determination and aggression in their game, especially in the second half to carry the day and become winners of the trophy for the fifth time.