The 31-year-old was forced to pull out of the Germany squad 10 days ago with a calf problem and missed the friendly win against England and the World Cup qualifying victory over Azerbaijan.
This latest setback will keep the goalkeeper out of the upcoming Bundesliga games against Augsburg on Saturday and Hoffenheim on Tuesday.
A statement on Bayern's official website read: "Due to a training injury on the left foot, a minor intervention by Professor Dr. Markus Walther was necessary on Wednesday evening with Manuel Neuer."
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Neuer has played in every Bundesliga game for Bayern this season to help the reigning champions pull 13 points clear at the top of the table after 25 games.
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