Arsenal are facing a humiliating last 16 Champions League exit for the seventh successive season after they succumbed to a second half goal-rush from Germany’s finest.
For most clubs just reaching this level so consistently would be regarded a success, but the lack of progress from this stage has become a stick with which to beat Arsenal manager Arsene Wenger.
And the manner of this defeat, with the second leg to come in London on 7 March, is what will damage Wenger’s standing the most as they went from 1-1 at half-time to all but out of the competition 15 minutes later.
Arsenal recovered from conceding an early Arjen Robben wonder goal before Alexis Sanchez equalised after 30 minutes with Bayern finishing the first period on the back foot, despite dominating possession.
This is the fourth time Bayern and Arsenal have met at this stage of the competition since 2005, with the German side progressing on the past three occasions.
They also won 5-1 here when Arsenal visited last season for a group game.
And maybe the Gunners were mindful of that after the break as the loss of captain Laurent Koscielny to injury sparked a dramatic collapse with Robert Lewandowski heading in scoring before a brutal double strike from Thiago.
Thomas Muller made it five from the bench, but it could have been so many more but for a great display from Arsenal keeper David Ospina, selected ahead of Petr Cech.
Arsenal started well, but Bayern passed their way into control of possession and the combination of Philipp Lahm and Robben seemed to have it all their way as they attacked down Arsenal’s left.
Then came a moment of brilliance from Robben to break the deadlock in the 11th minute.
The former Chelsea man took the ball from the corner of Arsenal’s area and players such as Francis Coquelin and Mesut Ozil failed to close down the Dutchman before he whipped an unstoppable shot into Ospina’s top right-hand corner.
Wenger’s plan of keeping it tight were already destroyed and his night was only to get worse as his 20th year at Arsenal is increasingly looking like it could be his last. This was always likely to be a match when his men had less of the ball, but they could hardly get close to it now.
Their only ray of hope came in the pace of Sanchez on the break and the Chilean drew a deliberate trip and yellow card for Mats Hummels midway through the first half. Ozil’s free kick nearly led to a goal, but the real chance came moments later when Lewandowski clattered Koscielny to concede a penalty.
Sanchez is not a great penalty taker, but he insists on taking them. Manuel Neur parried his spot-kick, the Arsenal striker mishit hit the rebound, before rattling home at the third time of asking, with five Bayern players challenging him for the ball.
Sanchez seemed to be about the only Arsenal player with genuine belief, however, and the home team were soon back in control as the atmosphere went up yet another notch in an exhilarating Allianz Arena.
And for all their time on the ball, Bayern still struggled to test Ospina again before Arsenal had the best chance to score again. This time Ozil, Sanchez and Alex Oxlade-Chamberlain combined well to set-up the recalled Granit Xhaka from 18 yards.
Penalty culprit Lewandowski then squandered a great opportunity to restore his side’s lead only to head over the bar shortly before half-time. Hummels also went close in the air from a set-piece.
But Arsenal ended on top with Ozil not making the most of a chance with only Neuer to beat. At least he drew a save from his old schoolmate to record his side’s fifth attempt on target, compared to Bayern’s three.
Goals win matches, though and Arsenal’s plans suffered a severe blow just three minutes after the restart when captain and best defender Koscielny suffered a hamstring injury denying a Lewandowski break.
He was immediately replaced by Gabriel with Kieran Gibbs adopting the armband.
Five minutes later, and Lewandowski out-jumped Mustafi to an inch-perfect Lahm cross to score with a superb header.
Bayern’s third was breathtakingly brilliant — fewer than three minutes later — as Thiago played a scintillating one-two with Lewandowski before running clear for an easy finish.
There could and should have been another on the hour as the big Polish striker clipped the bar and Gibbs appeared to save Robben’s rebound effort with a hand.
Ospina then made a world class save from Javi Martinez before man of the match Thiago benefited from a deflection to make it a deserved fourth home goal in the 63rd minute.
Koscielny’s departure had triggered a collapse and Wenger finally attempted to close the goal-gap by sending on Theo Walcott for Iwobi. Olivier Giroud also came on but it was Ospina who remained the busiest player on the pitch.
The only late ray of light for Arsenal was a booking to the irrepressible Lahm who’s booking means he will miss the second leg.
But Bayern manager Carlo Ancelotti knows he could probably afford to rest any of his players after watching super sub Thomas Muller rattle in number five with a minute to go.
Kimmich for Douglas Costa 84, Muller for Lewandowski 86, Rafinha for Robben 88.
Gabriel for Koscielny 49, Walcott for Iwobi 66, Giroud for Coquelin 77.
Milorad Mazic (Serbia).