Lennart Karl had levelled the game in the first half, but Arsenal went through the gears after the break to secure the win.
Arsenal are now sat top of this season’s Champions League league phase table and are the only side still boasting a 100 per cent record in the competition.
Standard Sport’s Simon Collings was at the Emirates to pick out three key talking points…
Madueke and Martinelli make their mark
Arsenal have been stretched in attack over the past few weeks, but the cavalry have arrived.
At 1-1 this game was in the balance, however Mikel Arteta’s substitutes made the difference within a minute of his changes.
Riccardo Calafiori, on at left-back, got down the flank and his cross was tapped home by Madueke.
The England winger had been brought on in the first half, after Leandro Trossard went off injured, but he had only moved to the right flank after Bukayo Saka had been substituted as part of the double change that also saw Calafiori come on.
Saka had been taken off for Martinelli, and he was the scorer of Arsenal’s third goal which wrapped up the game.
The Brazilian started the move by winning the ball inside his own area, before charging forward to expose Bayern’s high defensive line.
Eberechi Eze clipped a deft ball over the top and Martinelli rounded a stranded Manuel Neuer to put the game to bed.
Arsenal have been without Madueke since September due to a knee injury, while Martinelli has been absent for a month with a groin strain.
Ahead of the busy festive period, their returns are a huge boost for Arteta.
Rice rises to the occasion
Bayern’s midfield may have controlled the possession for much of this match, finishing it with a shade over 60 per cent, but it was Rice who ran the show.
The England star has been in brilliant form all season and he was at his best again here as he drove the team forward.
Rice snapped into tackles and was at the heart of Arsenal’s display, winning the ball for the vital second goal.
The only blot on the midfielder’s copybook was that he did not get on the scoresheet himself, denied after a lung-busting run forward by a good save from Neuer.
Other than that, this was an imperious performance from Rice, who looks all set for a monster showdown with Chelsea’s Moises Caicedo on Sunday.
Mosquera puts his hand up
Much of the talk before this game was about Bayern’s blistering attack and Harry Kane’s red-hot form.
There was a feeling that the Bundesliga leaders could get at Arsenal, who are currently without the injured Gabriel.
Arteta’s solution last weekend for the north London derby had been to turn to Piero Hincapie, who performed well on his Premier League debut.
This time, however, Cristhian Mosquera was given the nod and he slotted in alongside William Saliba in the heart of defence.
Mosquera has made an excellent start to life at Arsenal and is making a mockery of the £13million fee the Gunners paid Valencia for him.
The 21-year-old was on fine form again here, putting in an assured display and keeping Kane quiet.
Mosquera looked at home on the big stage and it would appear that Arteta now has two options as he works out how to cope without Gabriel.
