André Villas-Boas told a special press conference on Tuesday that he wants to leave Olympique Marseille.
The 43-year-old trainer is angry that a player has been signed on Deadline Day without his knowledge.
"I submitted my resignation this morning. On the grounds that I do not agree with the sporting policy," said Villas-Boas.
"I have not yet received an answer from the board. I don't need anything from Olympique Marseille. I don't want any money, I just want to leave."
The number nine of the Ligue 1 announced just before midnight on Monday that Olivier Ntcham has been recorded.
The 24-year-old midfielder is rented from Celtic until the end of the season.
"This decision was not made by me, I have nothing to do with it. I heard it through the media this morning," said Villas-Boas.
"He's a player I said 'no' to. He wasn't on our list. I can't accept this."
The Portuguese emphasized that his decision has nothing to do with Saturday's events.
The game against Stade Rennes was postponed after the Olympique training complex was stormed by angry fans.
About three hundred supporters started a fire at the entrance to the training complex.
They also lit fireworks and windows were broken.
Olympique Marseille will visit RC Lens in the competition on Wednesday.
It is still unclear whether Villas-Boas will be sitting on the couch by then.
Hard core pelts Marseille training complex with fireworks