Muller struck a brace in Bayern's 4-0 thrashing of Hannover on Sunday before coming off just after the hour-mark.
Bayern chief medical officer Hans-Wilhelm Muller-Wohlfahrt has ordered Muller to rest for five days before resuming light training.
It rules him out of Saturday's encounter against fourth-placed Schalke.
Muller could return against Wolfsburg on March 8, or head coach Pep Guardiola may opt for caution and leave him out until the UEFA Champions League clash against Arsenal three days later.
The 24-year-old was on the scoresheet in Bayern's 2-0 win at Arsenal in the first leg of their last 16 tie.
In good news for the reigning Bundesliga and European champions, Franck Ribery and Xherdan Shaqiri are close to returning.
Ribery, who underwent surgery on a buttock problem earlier in February, completed a double workout, including sprints.
Shaqiri is set to resume normal training later this week, nine days after tearing a muscle against Freiburg.
