Rather than criticise his players for another mauling by the ruthless German side, Wenger directed his frustration at Greek official Tasos Sidiropoulos whose performance he called "scandalous" after Arsenal had suffered a 10-2 aggregate defeat.
Wenger, out of contract at the end of the season and seemingly edging towards the exit door after nearly 21 years in charge, was angry that Theo Walcott was denied a penalty shortly after his goal had fuelled hope of a miraculous comeback.
He accused Sidiropoulos of "killing" his side when sending off skipper Laurent Koscielny after the defender had conceded the penalty from which Robert Lewandowski levelled.
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"I felt that we produced a performance with spirit and pride that we wanted and after that the story finished badly," Wenger, who has now presided over seven consecutive last-16 exits in the Champions League, told reporters.
"We were unlucky tonight at 1-0 in the first half with a definite penalty on Walcott and in the second half the referee killed the game. After that it was very difficult," the Frenchman added.
"The referee was very powerful tonight. Not only was it not a penalty but (Lewandowski) was also offside. On top of that he gives us a red card that killed us completely.
"I think it was unexplainable, it's scandalous. Bayern are a good side but tonight they can say thanks to the referee."
Wenger's team have lost three of their last four Premier League games to slip out of the top four and some fans held banners calling on him to go at the end of the season.
"Stubborn, Stale, Clueless" read one placard while chants of "Arsene Wenger We Want You To Go" could be heard outside the ground.
Wenger, 67, cut a forlorn figure as Bayern ran riot in the final 20 minutes with Arjen Robben, Douglas Costa and two goals from Arturo Vidal inflicting their biggest home defeat for 19 years.
"The players did not let me down, the referee let us down," Wenger said, rejecting any idea that his players had given up.
"We were in an impossible situation at 1-1 with 10 men, to have to score four goals against a team with their quality. We had to try but knew we would be hit on the counter-attack. If we didn't go forward people would ask why.
"The final 20 minutes was difficult. We had no hope and Bayern can bring fresh players on."
Arsenal can redeem themselves in this weekend's FA Cup quarter-final against fifth-tier Lincoln City but even lifting that trophy might not save Wenger.
Former Arsenal striker Ian Wright believes Wenger's long reign at the London club is nearly over.
"With everything that's going on you have to say it will take some sort of monumental effort for Arsenal to turn it around in terms of the drive and determination of the players," Wright said.
"It feels like something is coming to an end."
(Editing by Ed Osmond)
