Robert Lewandowski needed 10 minutes to head the hosts in front before a brace for Thomas Muller and goals from David Alaba and substitute Arjen Robben wrapped up a convincing 5-1 win for Bayern.
Arsenal had a potential Mesut Ozil equaliser correctly ruled out for offside as Olivier Giroud pulled one back for the Premier League side but by that time they were four goals behind having been torn apart by a rampant Munich frontline.
The result means Arsenal have lost three of their four Group F fixtures and sit bottom of the group – with wins in their remaining two matches not enough to guarantee progression.
Wenger’s cause was not helped here as both Hector Bellerin and Laurent Koscielny were ruled out with injuries – and the two players drafted into the Gunners defence were culpable.
Gabriel partnered Per Mertesacker at the heart of the defence but played Lewandowski onside for the opener while Mathieu Debuchy completely missed a Philipp Lahm cross that led to Muller doubling the lead.
And Wenger was in no mood to sugar-coat his side’s deficiencies at the back as he saw Arsenal suffer their heaviest Champions League defeat in their history.
“I believe first you have to give credit to Bayern for their quality and on top of that we made things quite easy for them with our defensive performance,” he said.
“We were extremely poor defensively and were not at the races. The funny thing was that when we went forward every time we looked like we could create chances but with a defensive performance like that you are going nowhere.”
Wenger stopped short of labelling the performance the worst defensive display of his lengthening tenure and admits progression into the knockout rounds is looking unlikely.
“My memory is not good enough to tell you in 19 years if it is not the worst performance,” he said.
“It will certainly not remain in my memory for anything positive.
“There is still a chance to qualify, Olympiacos have to lose here, we have to beat Zagreb and then beat Olympiacos in Olympiacos, there is a small chance but it is a real one.
“We have to realise with the kind of performance we have today that our chance is at a minimum.”
A north London derby at home to rivals Tottenham on Sunday could prove the perfect tonic for Wenger and his players as they look to keep up the pace at the top of the Premier League.
The Frenchman is focused now on that fixture, although he did admit his players may suffer psychologically after this drubbing.
“No matter how many we have, we have to give it all for a chance to qualify,” he added.
“Anyway we now focus on the championship on Sunday and turn up with a different performance, we are in a strong position in the league because if we play like we did today we are going nowhere.
“Bellerin I don’t think will be available for Sunday and Koscielny has a small chance. From tonight we have no more injuries, apart from in their heads we have no more injuries.”
Thanks to a late Olympiacos winner against Dynamo Zagreb, Arsenal now need the Greek side to lose in Munich in a fortnight for them to stand any chance of getting out of the group.
A draw here would put both Munich and Olympiacos through, but Pep Guardiola insists his Bayern side will be looking for the win to sew up top spot.
“You make this question to a coach and a club then you have to know it is impossible to not try and win the game,” he said when asked if he could assure Arsenal his side will not settle for a draw.
“Arsenal fans need to be calm. The players are going to go and try to win against Olympiacos, we might not be able to do that but not because we weren’t fighting but we want to be first in the group.”