A group of fans kicked and punched Bajevic during a pre-season friendly on August 8 and a section of the crowd threw seats towards him after Sunday's defeat, although none hit him.
It was the 61-year-old Serbian's third stint in charge of the club, but a group of the fans are apparently enraged by his previous job coaching rivals Olympiakos.
He told reporters at a post match news conference: "I will not be talking about the game, what I can say is that I have informed the president and the players that I have resigned."
LATEST ARTICLES
