The Germany international has sustained a "minor muscle problem" and will not be risked for the game against last season's beaten finalists at the Allianz Arena.
"He has some discomfort and he will miss out," head coach Carlo Ancelotti told a news conference. "It's a minor muscle problem."
Ancelotti also confirmed that attacking duo Julian Green and Kingsley Coman are not fit to be involved, but Holger Badstuber and Xabi Alonso should both be available.
Ancelotti said he is prepared to make a number of changes to the side that beat Mainz 3-1 in the Bundesliga last Friday, with Bayern already guaranteed to progress from Group D in second place, behind Atletico.
"The team has the quality to play in different formations and how we set up will depend on the game we're playing," he said.
"We've won two games in the Bundesliga and we want to pick up some more confidence with a result against Atletico."