Arsene Wenger's side hosts the reining European champions, who have lost just two games in all competitions this season, at the Emirates Stadium on Wednesday.
Arsenal was knocked out in the round of 16 last season by Bayern and Mertesacker hopes his teammates have learned from their exit from the competition.
"We have to go for two perfect games against them. We know we can beat them now, so maybe mentally we are in a better condition that last year," Mertesacker told reporters. "We respected them too much in the first leg then, so it was too easy for them. Maybe we have learned something from those lessons and will do better this time.
"Now we have another chance — and an opportunity to beat the champions. We want to achieve something exceptional this season, so we have to beat the best. That is not only Manchester City and Chelsea. That is Bayern Munich in the Champions League."
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