The two goals came in a seven-minute burst in the second half as Cameroon finally converted their superiority into goals in front of an ecstatic crowd at the Japoma Stadium.
Toko Ekambi got his first with a 50th minute header and then, in the 57th minute, snuck in behind the Gambian defence to tap home a square pass for the second.
The tournament hosts completely dominated the encounter against Gambia, who, at 150 in the FIFA rankings, were the lowest-rank team coming into the 24-team tournament.
Gambia, making their debut at the finals, had upset wins over Tunisia and Guinea on their way to the last eight but were almost anonymous on Saturday as they saw little of the ball and spent almost all of the match on the back foot.
Had Cameroon made better use of their opportunities, the scoreline might have been more emphatic.
Aboubakar had three good first-half chances to open the score and add to his tournament goal tally of six.
The first was an attempted backheel and the next two were headers from close range.
He did well to get ahead of youthful defender Joe Gomez but put his first headed effort wide while the second was saved at point-blank range by Baboucar Gaye in Gambia's goal.
But Toko Ekambi made no mistake when he got his chance from Samuel Oum Gouet's cross, glancing his header wide of Gaye and into the net.
He then ran off the defence and into space to add a second goal with a tap-in at the back post and now has five goals for the tournament.
Gambia had a little more possession after the second goal but never threatened the Cameroon goal.
Later on Saturday, Burkina Faso take on Tunisia in their quarterfinal in Garoua.