The 28-year-old replaced James Rodriguez at the start of the second half at the Volksparkstadion on Saturday, only to be forced off the pitch three minutes after setting up Corentin Tolisso's match-winning goal.
The extent of the damage is as yet unknown, but Bayern head coach Jupp Heynckes is cautiously optimistic that the injury is nothing too serious.
"First things first is a scan," Heynckes told Sky after the game. "Thomas said that it's cramp, or rather a muscle hardening. I hope that's all it is."
Müller has been integral to Bayern's resurgence under Heynckes, laying on goals against Freiburg and Hamburg, and scoring in the 3-0 win over Celtic in the UEFA Champions League. His assist for Tolisso was his 100th in the Bundesliga.
Watch: Thomas Müller, aka the Space Invader
Bayern return to action on Wednesday, when they take on Bundesliga title rivals RB Leipzig at the Red Bull Arena in the second round of the DFB Cup.