Hoeness tendered his resignation as president and chairman earlier on Friday, after receiving a three-and-a-half-year prison sentence for tax evasion on Thursday.
The 62-year-old said he fully accepted the decision and would not appeal the sentence administered by a German court.
Initially Hoeness was charged with defrauding authorities of €3.5 million, however at his trial in Munich the actual figure was revealed to be €27.2m.
Hoeness brought the evasion to the attention of authorities last year, in a move his defence team hoped would mitigate any punishment.
But - following three days of hearings - Hoeness was found guilty of seven counts of tax evasion and decided to relinquish his post at Bayern.
Hainer, currently deputy chairman, now takes the role of chairman "until further notice".
A statement on Bayern's official website read: "Herbert Hainer (59), adidas AG CEO and previously deputy chairman of the FC Bayern Munich AG supervisory board, is appointed chairman of the supervisory board, effective immediately and until further notice. This decision was unanimously approved by the supervisory board."
Upon the announcement, Hainer paid tribute to Hoeness' legacy.
"Uli Hoeness hhas always devoted his leadership qualities, great personal commitment and outstanding lifelong effort to the best interests of FC Bayern Munich," he said.
"He is very largely responsible for FC Bayern Munich becoming one of the most successful and attractive clubs in the world both in sporting and financial terms. We offer him heartfelt thanks and gratitude for this."
