Toni Kroos and Thomas Muller put the 2012 runners-up two goals ahead after 20 minutes but Lukas Podolski gave the hosts hope with a 55th minute reply.
Just when Arsenal were starting to gain a foothold in the match as they searched for the equaliser, Mario Mandzukic luckily looped the ball over the line with 13 minutes left to re-establish the German side’s dominance.
The Frenchman had recalled his big guns as he made seven changes from the team that were dumped out of the FA Cup by Blackburn Rovers at the weekend, with Theo Walcott spearheading the attack in place of the axed Olivier Giroud.
Arsenal came flying out of the starting blocks as they took the game to Bayern but the visitors dealt them a crushing blow after seven minutes with a slickly-constructed opening goal.
Dozy defending from the hosts allowed Thomas Muller’s mis-hit cross from the right flank to be seized upon by Kroos on the edge of the penalty area. The 23-year-old demonstrated terrific technique to smash the fizzing cross into the ground and over Wojciech Szczesny into the goal.
|BATTERED BY BAYERN
|COMMENT: Arsenal at crisis point as Wenger plays same old broken record|
Daniel van Buyten latched on to a near-post corner to flash a header straight at Szczesny, who should have done better than weakly parry the ball barely a yard in front of him. While the red-and-white shirts crammed into the six-yard box barely moved, Muller pounced to prod the ball home.
With just 20 minutes of the tie played, Arsenal found themselves teetering on the brink of a Champions League exit.
Wenger’s team were shell-shocked at going two goals down and struggled to mount an attack of note in the remainder of the opening period against one of the meanest defences in Europe.
A combination of jeers and silence from the home support greeted the half-time whistle but Wenger’s team talk did not appear to have much initial effect as the second period carried on from where the first had finished.
In the 55th minute, Arsenal tip-toed back into the game as Bayern conceded a goal that was even softer than the second of the match.
After winning a fortuitous corner, Jack Wilshere’s curled ball was inexplicably allowed to travel into the path of Podolski, who directed it over an unmanned line with what appeared to be his shoulder.
Finally, die Roten had conceded a goal after 664 minutes of shutting out their opponents. Finally, Arsenal had some momentum.
Substitute Giroud nearly scored with his first touch after seizing open a fabulous cross from Walcott but, with 13 minutes remaining, Bayern re-established their two-goal advantage.
More hideous defending from the home team allowed a drilled cross from Phillip Lahm to fizz across the box and, in what seemed like slow motion, Mandzukic beat Bacary Sagna to the cross to send the ball looping cruelly over Szczesny and into the net.
The Gunners will now have to overturn a two-goal deficit, with Bayern enjoying three away goals to their name, when the sides meet for the second leg at the Allianz Arena on March 13.