The Champions League holders were pushed to the brink of elimination by the Gunners at the same stage of last season's competition, going through on away goals despite a 2-0 scare at home.
If they are to become the first side successfully to defend their title, they must get the better of Arsene Wenger's men once again, with the same formula of the first leg taking place at the Emirates Stadium, and the return at the Allianz Arena.
"There were more comfortable and easier opponents in the bowl, but we can't change it," Rummenigge said on his club's website.
"We know that they are opponents who we've got to treat with the utmost respect, and that is what we will do.
"We're going to have to play two great games."
Bayern are currently preparing to face Guangzhou Evergrande in the semi-final of the World Club Cup in Morocco, but they did not miss the draw with former Manchester City defender Jerome Boateng admitting it was not the result he wanted.
"It's the toughest draw we could have got," said the Germany international.
"They're going to be really motivated after what happened last year and they're going to be two very intense games."