Bayern -- who have reached the final of the past two Champions League campaigns -- were held 1-1 in Munich by Arsenal, but just as they did last year against the same opposition at the same stage, the Germans went through, this time 3-1 on aggregate yesterday.
However Bayern's joy at going through was somewhat soured after Arsenal coach Arsene Wenger accused Dutch wing Arjen Robben of diving throughout the two legs.
Robben, who won a penalty for Bayern in the first leg which saw the Arsenal goalkeeper sent off, was dismissive of the remarks.
"Great managers don't need to resort to claims like that. I don't want to have to defend myself against remarks like that," he said.
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Guardiola, who has won the trophy twice as coach of Barcelona, looked annoyed when told about the comments.
"The best team won over the two legs that is what happened," he said.
It left Italy without a side remaining in the competition as Napoli and Juventus went out in the group stage.
Simeone, a former combative Argentinian international midfielder who was capped over 100 times, said he was proud of his side and tried to play down expectations by saying Atletico were very much the underdogs still.