Muller-Wohlfahrt revealed on Thursday that he had stepped down from his position, citing a break in "the bond of trust" after feeling his medical team were blamed for injury-ravaged Bayern's quarter-final first leg reverse at Estadio do Dragao.
And a statement on Bayern's official website read: "FC Bayern Munich notes with regret the decision of chief medical officer Dr Hans-Wilhelm Muller-Wohlfahrt  to resign his medical duties at the club.
"Dr Muller-Wohlfahrt in particular, but also his team, have performed first-class work for the club and its players over the years. Our sincere thanks are due for this.
"FC Bayern will shortly announce new arrangements for the club's medical unit. Until then Dr Volker Braun, sports physician and consulting physician in trauma surgery and orthopaedics, will support the FC Bayern team at matches."
Muller-Wohlfahrt - renowned as a world leader in the treatment of sports injuries - is also the doctor for the German national team and has been associated with Bayern for nearly 40 years.
He previously resigned his position in 2008 following a row with then-coach Jurgen Klinsmann, only to return when the ex-Germany international departed the club.
In a press conference on Friday, Bayern's current coach, Pep Guardiola, played down suggestions of a fall-out between himself and Muller-Wohlfahrt.
Asked what had happened between the two, Guardiola replied: "Nothing. It was his decision to leave and I respect it."
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