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The World Cup winner has struggled for form in front of goal this season.
The 27-year-old was also on the bench for their final Champions League group game against Atletico Madrid and key Bundesliga clash against RB Leipzig in December.
Thiago Alcantara is set to play in an attacking midfield role with Douglas Costa taking Mueller's place on the left wing, Arjen Robben on the right and Robert Lewandowski as striker.
Alexis Sanchez is preferred to Oliver Giroud up front for Arsenal with Alex Iwobi and Alex Oxlade-Chamberlain on the flanks.
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Mesut Ozil, who has struggled for form in recent weeks and not scored since December, keeps his place and in-form David Ospina is preferred in goal to Petr Cech.
Starting line-ups for the UEFA Champions League last 16 first leg between Bayern Munich and Arsenal at the Allianz Arena on Wednesday (kick-off 1945 GMT):
Bayern Munich (4-2-3-1): Manuel Neuer; Philipp Lahm, Javi Martinez, Mats Hummels, David Alaba; Arturo Vidal, Xabi Alonso; Arjen Robben, Thiago Alcantara, Douglas Costa; Robert Lewandowski
Coach: Carlo Ancelotti (ITA)
Arsenal (4-2-3-1): David Ospina; Hector Bellerin, Shkodran Mustafi, Laurent Koscielny, Kieran Gibbs; Granit Xhaka, Francis Coquelin; Alex Iwobi, Mesut Ozil, Alex Oxlade-Chamberlain; Alexis Sanchez
Coach: Arsene Wenger (FRA)
Referee: Milorad Mazic (SRB)