The Bundesliga champions came into the second leg of the round-of-16 tie with a 5-1 win.
The Gunners needed four unreplied goals to pull off a miracle. They opened scoring through Theo Walcott’s emphatic finish.
However, the match turned quickly on its head, after captain Laurent Koscielny was sent off and a penalty was awarded to the visitors. Robert Lewandowski stepped up and equalized.
Arsenal collapsed once again and further goals from Arjen Robben, Douglas Costa and Arturo Vidal (twice) completed a miserable night for Wenger’s team.
“The second half of the game has been ruined by the referee,” Wenger told BT Sport.
“Lewandowski is offside, then a yellow card, on top of that he gives a red card. It’s not serious. It’s revolting.
“My team has produced a huge effort tonight. It’s difficult to understand what’s happened tonight.
“I’m sorry for people coming paying their money to see this sort of game.”