Jesus, 67, referred to "the end of the Ozil era" when speaking to the press for the first time since his appointment, and suggested it was in the best interests of the club for the former Arsenal man not to feature again.
Former Arsenal midfielder Ozil has not played for the Turkish Super Lig side since March 20 after he was excluded from the squad following a row with interim head coach Ismail Kartal over his fitness.
Kartal did not get the managerial job permanently, but Jesus has pledged to follow in the 60-year-old's footsteps and keep Ozil away from the starting XI.
"He had his time, his space," Jesus said on Wednesday.
"He has a beautiful history in Turkey, nobody can take it away from him.
"He is a well-known player around the world. But I will follow exactly what was the end of the Ozil era.
"The most important thing here is not the coach Jorge Jesus, the most important thing here is not the player Ozil, the most important thing here is not any player.
"The most important thing here is Fenerbahce and it is from there that I build my ideas and the players who come to work with me."