Toni Kroos and Thomas Muller scored the goals in the second half but only after Wojciech Szczesny was sent off just before half-time after a collision with Arjen Robben.
In a wild first 45 minutes both sides missed penalties, but the Gunners will now have to travel to Munich again needing a miracle to keep their slim Champions League hopes alive.
Kroos, who was outstanding throughout, kicked off proceedings - bringing out the best in Szczesny inside five minutes. His beautifully struck drive was arrowing into the top corner only for the Polish international to flick it over one-handed.
Despite the near miss, Arsenal started the game well on top. And a fantastic Jack Wilshere through ball conjured the Gunners’ first opportunity.
Mesut Ozil was upended by Germany teammate Jerome Boeteng - a clear penalty and yellow card for the former Manchester City player. But the £42.4m man was foiled by his childhood friend, Manuel Neuer.
The two had grown up together, had even played for the same youth team together in Gelsenkirchen. The slow, lazy run-up, the placement, Neuer had doubtless seen it all before - and he quitened a noisy Arsenal crowd with a comfortable penalty save.
Arsenal invested so much in that frantic first 15 minutes, you really felt they needed to score at least once to justify it.
And with a creeping inevitability, Bayern edged their way into the game. By the half hour mark they were well on top. Mario Gotze and Philipp Lahm were combining to good effect on the right while Robben floated menacingly behind Mario Mandzukic.
But it was Toni Kroos who was pulling the strings. And the reported Manchester United target was the man to unlock the Gunners defence on 40 minutes, flicking a delightful ball over the top to an onrushing Robben.
Szczesny committed, sent the Dutchman flying and was sent off. Penalty - yes. Red card - probably. Game over? Not quite.
Santi Cazorla was sacrificed and Lukasz Fabianski summoned. But David Alaba made it easy for the replacement, clipping the outside of the post. Another penalty miss and a breathless first half ended 0-0. Don’t ask me how.
Still, Arsenal fans surely feared the worst heading into the second period. Manchester City had kept Barcelona to two after Martin Demichelis saw red on Tuesday night. But Pellegrini's side may have let the tie escape with that late Dani Alves goal. The goal for the Gunners would be to keep it competitive heading to Munich.
Pep Guardiola wasted little time adapting his side to the change in the state in play - Boateng was withdrawn, Rafinha slotted in at right back, Javi Martinez dropped into midfield and Lahm was tasked with holding centre ground.
The message was clear. Exploit the extra space out wide. And that’s exactly how Bayern took the lead - Lahm, afforded time in the right channel, cut inside from the flank and teed up the brilliant Kroos, who curled a superb side-foot finish home from 20 yards.
The central midfielder has been linked with Manchester United, and based on this evidence, United fans should lobby day and night to get Moyes to bring him to Old Trafford.
Everything he did had purpose, his passing, positioning and finishing was always on point. He started Bayern attacks, snuffed out Arsenal ones and produced a masterclass in possession-based central midfield play. He completed 96.7 per cent of his passes, including 127 in Arsenal's half - and these were not always safe and sideways.
The pattern for the second half was set with Szczesny’s sending off, and Bayern relentlessly pushed, pulled and probed in search of that second goal that in all likelihood would kill the tie.
They were made to wait, but their patience paid off when a Lahm cross was headed home by substitute Thomas Muller with five minutes to play.
It was cruel on Arsenal - especially Laurent Koscielny and Per Mertesacker who were both superb - but the Gunners were shattered after chasing a Bayern side that controlled 79 per cent possession.
Mesut Ozil in particular was a virtual passenger in the last 20 minutes. Never the most enthusiastic defender, he looked completely devoid of energy. Forced to shuttle up and down the wing, he offered little protection for an overmatched Nacho Monreal.
Arsene Wenger will question the decision to send off Szczesny, while it could have been so different had Ozil's penalty edged Arsenal ahead in a period during which they were completely dominant.
But the Gunners manager now needs to focus his attention on overturning a two-goal deficit at the Allianz Arena.
A hugely difficult task, but they proved it possible last season. Can they put in a comeback performance at the Allianz Arena, time will tell.
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