The 61-year-old made the move amid an ongoing investigation into tax evasion despite claiming last week that he will not step down before the Champions League final later this month.
"One of the topics discussed at Monday's regular scheduled meeting of the FC Bayern Munchen AG supervisory board in Munich was the fiscal case concerning supervisory board chairman Uli Hoeness," reads a statement on the club's official website.
"Addressing the supervisory board, Uli Hoeness offered to step down temporarily from the office of chairman of the supervisory board until the relevant authorities come to a decision on whether his voluntary self-disclosure exempts him from penalty. Uli Hoeness expressed regret about the matter and apologised to the board.
"In the interests of FC Bayern, the need to focus solely on achieving the club's further sporting goals in the Champions League final on 25 May and in the German cup final on 1 June 2013, and following intensive discussion, the FC Bayern Munchen AG supervisory board agreed by mutual consent that Uli Hoeness should continue to exercise the office of chairman of the FC Bayern München AG supervisory board. The supervisory board will continue to monitor the matter and will return to the subject once there are further developments."
Bayern will take on Borussia Dortmund in the Champions League final at London's Wembley Stadium.