The France international suffered a ligament strain in his left ankle during his side's 3-2 win over Fortuna Dusseldorf on Saturday.
Midfielder Bastian Schweinsteiger and defender Jerome Boateng, who are banned, will also miss the match at the Allianz Arena.
Bayern hold a 3-1 lead from the away leg, though, to put themselves in pole position for a place in the quarter-finals.
Bayern are also sweating on the fitness of Arjen Robben, who was not involved at the weekend because of a calf problem.
The German giants have plenty of strength in depth, though, with the likes of Luiz Gustavo and Xherdan Shaqiri ready to come in.