Goetze was taken off in the 35th minute and tests showed he had torn some adductor muscle fibre.
"Mario Goetze will be missing from Bayern for 10 to 12 weeks," the club said in a statement, adding the player was still being treated by German national team doctors in Leipzig where the game was played. Germany need a point in their last game against Georgia on Sunday to qualify for Euro 2016.
Bayern have been in scintillating form this season and are seven points clear at the top of the Bundesliga after winning their opening eight games and also lead their Champions League group with two wins out of two matches.
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The 23-year-old Goetze has played in 11 of the 12 matches in all competitions this season, having scored four goals.
Bayern play VfL Wolfsburg in the German Cup second round on Oct. 27, either side of their Champions League matches against Arsenal on Oct. 20 and Nov. 4.
(Reporting by Karolos Grohmann, editing by Pritha Sarkar)
