It was not clear how long the 29-year-old would be out of action for, but Bayern said the key midfielder would be operated on "soon" after attempts to treat the problem without surgery failed.
"The last few weeks have been very painful," Schweinsteiger said in a club statement. "I tried but I have reached a point when renewed surgery is unavoidable. I hope to be able to play without any pain after the surgery."
The Germany international, who will now miss the games in Milan and London on November 15 and 19 respectively, was ruled out for much of pre-season training after needing surgery following their treble-winning campaign last season.
He had only recently returned to top form and the setback is another blow for Pep Guardiola's injury-hit team, which had just welcomed back fellow holding midfielder Javi Martinez after two months out.
Record-breaking Bayern have already qualified for the Champions League knockout stage with four straight group wins as they aim to become the first team to successfully defend the trophy.
They are also leading the Bundesliga, a point ahead of Borussia Dortmund, and can set a record with their 37th game without defeat against Augsburg on Saturday.
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