In a stunning post-match press conference, the 65-year-old said that he 'won't be returning' to the club.
He said: "I stepped down from my duties this evening. I made this decision to clear the way for my club. I resigned while the path is still clear, with no intention of ever returning."
This was Kartal's fourth stint with the Super Lig club, all of which have been short. His latest tenure started in July, as he guided them into the Champions League League Phase. However, domestically, they have won two of four games, losing to Istanbul rivals Besiktas last weekend.
Minutes after the press conference, Fenerbahce president Aziz Yildirim told reporters that Kartal "continues in his role".
"Some fans threw a bottle at the coach's head this evening during the game. He is upset about it," Yildirim said.
"I just spoke to Ismail Kartal. He mentioned the bottle incident and he also complained about being under pressure."
Asked if Kartal had told him that he would stay, Yildirim said: "There's no need for him to say (openly) that he'd continue. I am his senior, I told him to continue and that's it. We are a family."
