It took 55 minutes for this evenly contested affair to see the first goal and it was no surprise that it came via Aboubakar as the Cameroon star had been irksome to the visitors' defence for most of the night
Aboubakar volleyed home the opener from the back post after Kayserispor struggled clearing a corner.
Umut Bulut drew the visitors level in the 64th minute before Andreas Beck scored an own goal in the 82nd minute to see Anadolu Yildizi go in front.
However, as Kayserispor looked set to secure a crucial three points, Aboubakar returned again. This time, the 25-year-old turned stunningly inside the box to beat two defenders and poked home his second of the night from close range in the 88th minute for his sixth league strike so far this campaign.
Since returning from the Nations Cup - where his goal was the decider in Cameroon's final victory - the FC Porto loanee has now scored five goals in his last seven competitive games for Besiktas.
Aboubakar has also kept his place in the Indomitable Lions’ squad for the upcoming friendlies with Tunisia and Guinea towards the end of the current month.