Now it was Arsenal which began to grow and only a wonderful reaction save from Manuel Neuer denied substitute Olivier Giroud an equalizer.
It proved to be a crucial moment as with 13 minutes remaining, Mario Mandzukic bundled home Philipp Lahm's cross to all but end Arsenal's hope of making the quarterfinal.
Bayern, which is unbeaten in 19 games since losing to Bayer Leverkusen on October 28 last year, will now expect to finish the job on March 13 in Munich.
"We expected a very big start from Arsenal here at home with the fans behind them," Bayern's Arjen Robben told ITV.
"I know from my time in England and we warned all of the players we have to be there from the first minute because there will be a storm going here at the Emirates Stadium.
"I think we did very well and of course if you score two goals you're in a great position."
Based on past results in the competition, Arsenal has just a 2.2% chance of progressing to the next stage -- but in Wilshere it has one player with great heart and determination.
It is little surprise that Barcelona's players are already beginning to voice their admiration of the midfielder in a similar way they did during the pursuit of Cesc Fabregas.
For now Wilshere remains at Arsenal and fully focused on the task in hand.
"In the second half, we stepped it up and it's unfortunate we didn't do that in the first half," Wilshere told ITV.
"I'm not sure why. Maybe it's a bit of nerves or anxiety, because we show what we can do when we play. We will look at it and try to put it right."
But while Wenger ponders a redesign, Bayern will surely only grow stronger.
For next season they will have their own artist and in Pep Guardiola, the former Barceloan coach, it will have a man who has produced one of the great works of modern football.
In the night's other game, Joao Moutinho's second half strike was enough to give Porto a 1-0 win over Malaga.
In a tight and cagey contest, Moutinho popped up six minutes after the break to take Alex Sandro's pass in his stride and fire home past Willy Caballero.
But Malaga coach Manuel Pellegrini is adamant his side can still prevail when the two teams meet again in three weeks time.
"Whether it is a good result or not we will see at the end of 180 minutes," Pellegrini told Spanish TV station TVE.
"To lose is never good, but losing by just the one goal is the best thing we can take from the game.
"For all the possession Porto had they didn't create many clear cut chances and even the goal itself is offside.
"You have to give credit to Porto for the way they pressed us all over the pitch, but we have to apply the same pressure in Malaga.
"We can still turn the tie around at La Rosaleda. We have demonstrated this year that we can compete with anyone."