Cenk Tosun’s 65th-minute effort seemed enough to see Besiktas through but Aboubakar stroke deep in stoppage time to put the match beyond Yesil Timsahlar.
Besiktas returned to the summit of the Turkish top tier with three matches left until the end of the season, but Istanbul Basaksehir are tight on the heels of Senol Gunes’ men, who can't afford a slip-up.
Aboubakar’s strike was his 10th of the campaign as he continues his trend of scoring crucial goals for Kara Kartallar. He has now scored 10 goals in 24 matches so far this campaign.
This is the third time in three different countries that the Yaounde-born attacker has reached double figures, having already done so with Lorient in France and with FC Porto in Portugal last season.
With the Indomitable Lions scheduled to take on another giant of African football, Morocco, in a 2019 Nations Cup qualifier next month, Hugo Broos will be expecting to call upon his most trusted soldiers, and the 25-year-old is an integral part of that group despite his substitute role at the Afcon.