The North London outfit crashed out of the FA Cup on Saturday following a 1-0 defeat to Blackburn Rovers at the Emirates, but Vermaelen has called on his teammates to leave the "disappointment" behind.
"Tuesday night is a totally different game, different league, different opponents, so we have to focus again after this disappointment," Vermaelen told the club's official website.
"We need to get good spirit in the team again, make sure we focus and maybe think about the game [against Blackburn] but not too much. We have to focus on Bayern Munich."
The round-of-16 first leg is hosted at the Emirates tomorrow.