Georges-Kevin Nkoudou put the visitors ahead when he converted the penalty in the 89th minute.
The stoppage time strike from Ajdin Hasic secured a crutical win for Besiktas in Kayseri.
Besiktas now lead the league with 31 points while Hes Kablo Kayserispor sit bottom of the table with 10 points in 15 matches.
Sunday's results in Super Lig:
Caykur Rizespor - Genclerbirligi: 1-1
Fatih Karagumruk - Trabzonspor: 1-2
Hes Kablo Kayserispor - Besiktas: 0-2
