The hosts made a shaky start before an unmarked Michael Ngadeu headed in Moumi Ngamaleu’s corner to put Cameroon ahead in the 13th minute.
Aboubakar doubled the lead 12 minutes later when he hooked in Ngamaleu’s cross following a well-worked short corner on the right.
Cape Verde puled one back eight minutes before the break when Jamiro Monteiro slotted Bebe’s through ball past the onrushing Onana.
But Cameroon restored their two-goal lead on the stroke of half-time, with Ngamaleu involved again as the Dynamo Moscow forward was brought down by Deroy Duarte and captain Aboubakar unerringly converted the resulting penalty.
The Indomitable Lions then made it 4-1 nine minutes into the second half when Nouhou Tolo held off centre-back Roberto Lopes to head home following another short corner.
In Saturday’s other qualifying tie The Gambia thrashed Seychelles 5-1 in neutral Morocco to register their first victory in Group F.
Northern Irishman Johnny McKinstry was taking charge of the Scorpions for the first time, and the game was level at the break after Ryan Henriette cancelled out Mohamed Badamosi’s opener for the West Africans.
Musa Barrow’s penalty restored the lead and Badamosi netted again in between efforts from Yankuba Minteh and St Johnstone forward Adama Sidibeh as The Gambia eased to victory.
The fourth round of qualifying matches will take place between Sunday and Tuesday.