A night that began with protests against Wenger ended with his side out of the competition in the round-of-16 for the seventh consecutive season after the embarrassing loss.
The emphatic defeat in the first leg three weeks ago left Arsenal with an uphill task against the German champions, but Theo Walcott's 20th-minute goal gave the hosts a glimmer of hope.
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Arsenal XI: Ospina; Bellerin, Mustafi, Koscielny, Monreal; Ramsey, Xhaka; Walcott, Oxlade-Chamberlain, Welbeck; Sanchez
Subs: Cech, Gibbs, Gabriel, Coquelin, Ozil, Lucas, Giroud
Bayern XI: Neuer, Rafinha, Martinez, Hummels, Alaba, Alonso, Vidal, Thiago, Ribery, Robben, Lewandowski
Subs: Ulreich, Costa, Bernat, Muller, Coman, Kimmich, Sanches
WHAT THEY SAID
Arsene Wenger: "What you expect is that you go out there with a mixture of lucid rage.
"Let’s not fool ourselves, we have a one or two per cent chance - but you never know."
Carlo Ancelotti: "Wenger is a manager with a lot of experience, more than others, and I’m sure he will be able to manage this situation.
"It’s a situation that can happen to every manager. Criticism is normal."