The Bundesliga champions have been beset by injuries in recent weeks and were missing Arjen Robben, Franck Ribery, David Alaba, Javi Martinez and Mehdi Benatia from the 3-1 loss to Porto on Wednesday.
Holger Badstuber and Bastian Schweinsteiger have also struggled with long-term injury problems in recent months and the Bavarians named just three outfield players among the substitutes for Saturday's Bundesliga win over Eintracht Frankfurt.
The long-serving 72-year-old has now confirmed he has resigned after bearing the brunt of the blame for the side's defeat in Portugal.
"After the Champions League match between Bayern Munich and Porto, the medical department was blamed due to the inexplicable reasons for the loss," Muller-Wohlfahrt said in a statement.
"The bond of trust is damaged."
Bayern's media director Markus Horwick confirmed the decision had taken the club by surprise, telling Sport1: "FC Bayern were not informed about this step."
Muller-Wohlfahrt left Bayern in 2008-09 after a falling-out with former head coach Jurgen Klinsmann only to be convinced to return following his departure.
Head coach Pep Guardiola admitted earlier this season he was becoming exasperated with the medical condition of some of his players, particularly defender Jerome Boateng.
"I must always replace Boateng before the match has finished," he said in September. "But we can't replace one defender in every match. Defenders normally have to play from the first to the last. We have to talk to the doctors another time."
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