The Croat, who has scored eight goals in the Bundesliga and another two in Europe this season, remained in Munich for treatment as the holders seek to seal top spot in Group D after already booking their ticket for the knockout stage.
"We need at least one point," club CEO Karl-Heinz Rummenigge told reporters on Tuesday before the team's departure.
"Then our position will be outstanding going into the last game against Manchester City because we want to win the group."
Mandzukic is the latest to join Bayern's injury list with Franck Ribery, Bastian Schweinsteiger, Xherdan Shaqiri, Claudio Pizarro and Diego Contento already ruled out.
Bayern, who advanced earlier this month with their fourth straight win in the group, have 12 points with two games left to play, three ahead of Manchester City in second.
"With a win we will be almost certain to top the group," said Rummenigge, whose team are seeking to become the first club to successfully defend the Champions League trophy.
(Reporting by Karolos Grohmann; Editing by Peter Rutherford)
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