The Gunners were thrashed in each of their two meetings with the Bundesliga title holders, bowing out of the Champions League's round of 16 after a humiliating 10-2 aggregate defeat.
They responded by easing past Lincoln City 5-0 to reach the FA Cup semi-finals on Saturday.
But after that routine win at Emirates Stadium, attention returned to one of the worst results of Wenger's tenure in north London, the Frenchman explaining the rationale behind sticking with many of the players who came unstuck against Bayern.
"I didn't want to gamble, I knew it was important to win the game," he told a post-match news conference.
"The team performed well against Bayern and I wanted to give them the chance to regain their confidence.
"The players didn't let me down. I think we had an outstanding performance as long as we were 11 versus 11."
According to Wenger, the decision of match official Anastasios Sidiropoulos to dismiss Laurent Koscielny in the 53rd minute sealed the Gunners' fate.
"We collapsed in the second half against Bayern, but when you are down to 10 men against a quality team... it is not a football game," he said.
"I wish you'd sit in my seat for a while and then you would realise it's impossible to keep everyone quiet. But we try.
"The criticism wasn't justified from our last match. I watched this game three times now and the referee killed the game."
Wenger confirmed Alex Oxlade-Chamberlain, who limped off in the first half against Lincoln, is suffering from a hamstring injury, but the manager is hopeful the problem does not prove to be too serious.