Head coach Vincent Kompany stated the Germany international might not be in a position to feature against the Gunners during his pre-match press conference and the call has now been confirmed.
Bayern said in a statement: "Due to a death in his immediate family, Joshua Kimmich is not in the squad today for the match against Arsenal.
"On behalf of the family, we ask his privacy and grief be respected, and that further inquiries and reporting be refrained from. In deep sympathy, the entire FC Bayern stands by Joshua Kimmich's side."
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Both sides will wear black armbands at the Allianz Arena with Kompany and Mikel Arteta winning their opening two matches of the competition this season against Napoli/Lille and Bodo/Glimt/Viking respectively.