Arsenal face an uphill task if they are to reach the quarter-finals of the Champions League, after Mario Mandzukic's fortuitous late strike ensured Bayern Munich returned to Germany with a 3-1 lead after the first leg.
Former Munich forward Lukas Podolski appeared to have given the Gunners hope when he turned home from a corner ten minutes into the second half, but Mandzukic bundled the ball home - thanks predominantly to a huge deflection off Bacary Sagna - from Philipp Lahm's low cross with 13 minutes remaining to restore the Bundesliga leaders' two-goal advantage.
Indeed, it took Bayern just 21 minutes to ease into a 2-0 lead - Toni Kroos scoring a beautiful volley past Wojciech Szczesny after seven minutes, before Thomas Muller was on hand to turn home after the Polish goalkeeper had barely kept out Daniel van Buyten's header not long after.
At the start of the match Theo Walcott's deployment as a central striker initially looked a sound tactical switch by Wenger as the England forward quickly got behind the Bayern defence, with Santi Cazorla also making good headway down the right.
However, the high-octane atmosphere from the home support fell flat as Bayern - some 15 points clear at the top of the Bundesliga - grabbed a crucial away goal on seven minutes. Muller's cross from the right was not dealt with and Kroos crashed the ball off the turf and past Szczesny from 18 yards.
Arsenal were shellshocked, but needed a response if they were to stand any chance of getting back into the tie. Bayern, though, continued to spray the ball across midfield, this time Franck Ribery picking out captain Philip Lahm on the overlap down the right, his cross put behind.
From the resulting corner, it was 2-0 and looked game over after just 21 minutes.
Van Buyten's header at the near post was parried by Szczesny, and Muller stabbed the ball straight back into the net from close range.
Arsenal were in danger of being overrun, with few cool heads as first Bacary Sagna and then Mikel Arteta were shown yellow cards for clumsy challenges.
There was finally some cause for concern in the Bayern penalty area when a deep free-kick was floated in from the right and Per Mertesacker's follow-up shot was blocked.
Lahm sent another teasing cross in from the right just before half-time which in-form Croatia striker Mandzukic planted wide with a free header from 12 yards.
Having left the field to a cacophony of boos from their own beleaguered fans, Arsenal needed to regroup at the break. The Gunners suddenly sparked into life on 55 minutes when Podolski, who had a disappointing three-season spell at Bayern, headed in Jack Wilshere's right-wing corner at the far post after
Goalkeeper Manuel Neuer - who had conceded just once in eight matches - decided to stay on his line. Bayern felt aggrieved at the award of the corner in the first place, as the ball looked to have deflected behind off the Arsenal striker.
The Germans, though, were soon back on the offensive as Kroos' angled, 20-yard drive was tipped over by Szczesny.
Bayern manager Jupp Heynckes made a change on 62 minutes as Dutch winger Arjen Robben replaced Ribery.
With 20 minutes left, Wenger produced a double switch as Olivier Giroud replaced Podolski and Czech midfielder Tomas Rosicky came on for Aaron Ramsey.
The France striker's first touch was to turn Walcott's superb right-wing cross goalwards, but unfortunately it was straight at Neuer.
It proved a crucial miss as Bayern scrambled in a tie-clinching third goal on 77 minutes. Robben sidestepped Vermaelen before releasing Lahm on the overlap down the right.
His cross flew through the six-yard box, where it Mandzukic got ahead of Sagna, the ball looping up off the Bayern striker's shin, over the goalkeeper and into the net.
In the night's other tie, Porto claimed a 1-0 advantage with a home win over Spanish side Malaga.
Midfielder Joao Moutinho scored the game's only goal shortly before the hour mark - the Portugal international slotted home Alex Sandro's pinpoint pass to earn Porto victory in a match of few clear-cut chances at the Estadio do Dragao.
The defeat was Malaga's first in their maiden Champions League campaign but Manuel Pellegrini's men will be hopeful of turning things round at La Rosaleda, where they beat AC Milan and Zenit St Petersburg in the group stages.
Two-time former European champions Porto will also be optimistic about their chances of going through to the quarter-finals, although they would have preferred a bigger advantage for the trip to Andalucia.