Izmir-based club's Ahmed Yasser Rayyan scored in the 14th minute at Ulker stadium in Istanbul, Fenerbahce's home ground.
Fenerbahce leveled the match with a close-range finish from Irfan Can Kahveci in the 37th minute.
Serdar Dursun then scored the winning goal with a powerful header assisted by Kahveci in the 71st minute.
Meanwhile, in another game, Trabzonspor were held to a 1-1 draw with GZT Giresunspor at the Senol Gunes Sports Complex in Trabzon.
Andreas Cornelius produced a goal for the Black Sea club, while Mehmet Umut Nayir scored the opening for the away side.
Trabzonspor failed to win the game when Greek forward Anastasios Bakasetas missed a stoppage-time penalty.
Fenerbahce are ranked third with 36 points, while Trabzonspor top the Super Lig with 51 points.
