Bayern have been missing a number of key players due to injuries in recent weeks, and Muller-Wohlfahrt suggested that his medical staff had been blamed for Wednesday's 3-1 loss to Porto in the first leg of the Champions League quarter-final tie.
However, Guardiola has responded to his departure by claiming that he had not confronted the doctor over the club's injury crisis.
"Nothing happened between us. It was his decision," the Spaniard told reporters. "I have great respect for him. I can only respect the decision. That is all."
Muller-Wohlfahrt has spent nearly 40 years with Bayern either side of a short spell away from the club after falling out with former head coach Jurgen Klinsmann in the 2008-09 season.