The 28-year-old, who scored the opening goal in the 3-0 win over the Hoops last week, picked up an injury at the weekend during the Bundesliga clash with Hamburg.
Bayern confirmed on Monday morning that Muller would be sidelined for three weeks after ‘straining his hamstring’ in the 1-0 win at the Volksparkstadion.
With an eye on Bayern’s next four fixtures, Jupp Heynckes had taken the decision to rest a number of players, including Muller, for the match against Hamburg.
Muller came on at half time for James Rodriguez but was replaced by Thiago just ten minutes later after sustaining the injury.
There had been fears that Muller had torn his hamstring, potentially keeping him out for six weeks, but Bayern allayed those concerns, confirming that it was just a strain.
Bayern face a trip to face RB Leipzig on Wednesday in the German Cup, before taking on Ralph Hassenhuttl’s side at the Allianz Arena three days later on league duty.
Heynckes will then take his team to Glasgow to face Celtic on the Tuesday night before another trip to Dortmund to face the current league leaders four days later.
Bayern are already without Manuel Neuer and Franck Ribery while the club are hopeful Mats Hummels will be fit to face RB Leipzig despite picking up an ankle knock.