The last 16 first leg loss exposed the lack of strength in depth which has contributed to the Londoners going out of both domestic cup competitions, lying fifth in the Premier League and looking poised to bow out of Europe.
Bundesliga leaders Bayern had the luxury of bringing on Dutch World Cup runner-up Arjen Robben and prolific Germany striker Mario Gomez in the second half but a glance at Arsenal's bench showed no such riches and Wenger's hands are largely tied.
"It's nothing to do with the manager - he puts us on the pitch, it's down to us to perform," he told reporters.
"The players have to take responsibility, we're man enough to take it. The manager has been here 16 years and he's done a great job so you can't question him."
However, celebrity fans such as British U.S talk show host Piers Morgan and golfer Ian Poulter are among those to have called for Wenger's departure and it is difficult to see what the manager can do to ease the pressure.
First-half strikes from Toni Kroos and Thomas Muller already had Arsenal against the wall but Mario Mandzukic's bizarre third goal after Lukas Podolski had pulled one back against his old club means last 16 progression looks impossible.
Not even a 2-0 win in Munich in three weeks' time will be enough, though that looks highly unlikely given Arsenal's current naivety in defence and fickleness in attack.
Thomas Vermaelen, still easily Arsenal's best centre-half despite some lapses this term, had to switch to left-back following Wenger's bungled attempts to fill the role and that left Per Mertesacker coming back into the heart of the backline.
Arsenal's best hope came from substitute Olivier Giroud, who had one decent chance to cut the deficit.
