With a growing number of fans demanding Wenger leaves at the end of the season, Arsenal suffered the ignominy of being handed a second drubbing by the German champions in the space of three weeks.
It was always going to be a virtually impossible ask to overturn a 5-1 deficit from the first leg as the odds of 33-1 before the game demonstrated.
But just like the first encounter, Arsenal capitulated in the second half after a promising opening 45 minutes, albeit they were not helped by Laurent Koscielny being sent off for a professional foul in the area.
The home supporters voted with their feet by leaving en masse long before the final whistle, while a section held up "Wenger out banners'. Others turned on owner Stan Kroenke by chanting 'get out of our club'.
The biggest cheer in the closing stages was when a fan invaded the pitch, it sums up how bad things have got.
Just like in Germany, there was no sign of the capitulation that was to come at the end of the first half.
The build-up to the game hadn't exactly gone smoothly. A poor performance in a defeat to Liverpool was then made worse by all the talk of relations between Alexis Sanchez turning sour.
There was also the sight of a pre-match protest from a section of supporters calling for Wenger to go.
As the two teams walked out empty seats were visible everywhere, while the atmosphere was terribly flat.
Still, with Sanchez back in the starting line-up, plus Theo Walcott and Aaron Ramsey recalled, Arsenal's attacking intent was clear.
And very soon the crowd went from being fairly subdued to actually upbeat as they saw their side showing some kind of threat.
Walcott, in particular, was a constant menace in the opening exchanges and should have given Arsenal an early lead, but wasn't able to control Sanchez's pass well enough.
Olivier Giroud, a late addition due to Danny Welbeck suffering an injury in the warm-up, struck the post with a header.
Remarkably Bayern looked a bit rattled, even more so as Walcott fired the ball over Manuel Neuer at the near post to give the north London club the lead.
This was exactly the kind of fight Wenger was talking about in his programme notes, on what was his 184th Champions League game as Arsenal manager.
Indeed, things could have got even better had Arsenal been awarded a penalty of Xabi Alonso's clumsy challenge on Walcott.
But it is typical of Arsenal's season that the same assistant referee behind the goal that ignored their claims on that occasion felt the need to intervene in the second half.
Koscielny appeared to only be booked when he fouled Robert Lewandowski in the area and a penalty was rightly awarded.
But referee Tasos Sidiropoulos seemed to then be convinced to send him off instead and Arsenal fell apart.
After Robert Lewandowski equalised from the spot in the 55th minute, Bayern ran riot.
Instead of a damage limitation exercise, Arsenal tried to play a high line with 10 men, as well as out from the back and it backfired spectacularly.
Arjen Robben, Douglas Costa and a brace from Arturo Vidal rubbed salt into what were already bitter wounds.
Boos ran out at the final whistle as the Champions League anthem played. Given Arsenal are also struggling to secure a top-four place in the Premier League, it may be a while before it's heard again at Emirates Stadium.
It certainly could be the final time Wenger gets to hear it as Arsenal coach.