The Germany international has been in inconsistent form in 2017, but will start as part of a three-man forward line at the Allianz Arena.
The Gunners have made two changes from their side that beat Hull City on Saturday, however, with David Ospina replacing Petr Cech in goal and Granit Xhaka comes in for Theo Walcott.
Bayern, meanwhile, have been boosted by the fitness of Xabi Alonso and Arjen Robben, who have both been passed fit to start following injury problems.
There is no place in the team for Thomas Muller, though, who must make do with a place on the substitute's bench.
Bayern Munich: Neuer; Lahm, Hummels, Martínez, Alaba; Xabi Alonso, Vidal; Robben, Thiago, Costa; Lewandowski.
Arsenal: Ospina; Bellerin, Mustafi, Koscielny, Gibbs; Oxlade-Chamberlain, Coquelin, Xhaka; Iwobi, Ozil, Alexis.