Arsenal failed to overturn their 2-0 deficit from the first leg three weeks ago, which still riles Wenger.
The Gunners finished with 10 men in London after Italian referee Nicola Rizzoli sent off Gunners goalkeeper Szczesny for conceding a spot-kick with a foul on Robben.
"Overall in the two games what made the difference was the decision to send our goalkeeper off," said Wenger.
"I felt it was not a red card as simple as that.
"Robben is very good at getting something out of nothing, he's a good diver, but that's part of his game.
"I have to congratulate the [Arsenal] players for their heart and effort.
"We wanted to come out of that tie qualified, but we came up short.
"Good luck to Bayern, but I think they are a bit more vulnerable than last season."
Robben angrily rebuked Wenger's diving claims.
"I expect more of great managers, they don't need to resort to claims like that," said the Dutch winger.
"I don't want to have to defend myself against remarks like that."
Arsenal midfielder Mesut Ozil, who failed to convert a crucial penalty in the first-leg, endured another miserable night in Munich.
The Germany attacking midfielder came off at half-time with hamstring trouble and made way for Tomas Rosicky.
Holders Bayern march on to the quarter-finals, but will be without Brazil defender Dante who picked up his third yellow card in Europe and is now suspended for the first leg.
Bayern boss Pep Guardiola was pleased that his side restricted Arsenal's scoring chances - only an Olivier Giroud header and Podolski's thunderbolt truly troubled the host's defence.
Atletico meanwhile left Italy without a side remaining in the competition as Napoli and Juventus went out in the group stage.
The result in Madrid never looked too much in doubt, once Diego Costa got the opener after three minutes, despite former Real Madrid star Kaka levelling halfway through the first-half.
Turkish international Arda Turan restored the one goal lead before the break with a half-volley that took a wicked deflection and Raul Garcia and Costa added two more in the second-half, the latter taking his tally this season to 29.
