Kocaman’s side overcame Trabzonspor 1-0 to lift the domestic trophy in Ankara last week, but the Turkish boss has decided to step down after missing out on the Super Lig title to Galatasaray.
The club announced they had accepted the coach's resignation with a brief statement released on their official website on Wednesday. No reason behind the decision was given, although there are reports that Kocaman had a disagreement with chairman Aziz Yildirim, who was reluctant to sell a number of foreign players within the squad.
In his three seasons in charge at the club, Kocaman guided them to two consecutive Turkish cups and a Super Lig title in 2010-11.
They have finished runners-up the last two seasons and were knocked out of the Europa League at the semi-final stage to Portuguese side Benfica, having made the last four in a European tournament for the first time in their history.