Pep Guardiola's side, joint top of the Bundesliga with Borussia Dortmund after six games, booked their place in the draw with a 5-0 hammering of fourth-tier outfit Schwarz-Weiss Rehden last month and will be high on confidence after hammering Schalke 4-0 in the top flight on Saturday.
Bayern won their 16th DFB-Pokal crown by beating Stuttgart in last season's final to complete an historic treble after also lifting the Bundesliga and UEFA Champions League titles.
Jurgen Klopp's side will visit their Bundesliga 2 opponents after winning 3-0 away at Wilhelmshaven in the opening round, and the manager has warned his players that their second-round tie would not be straightforward.
"They are a good football team," he said.
"They have every right to be unhappy with their situation. They're an ambitious club that want to climb up the table and get out of there (Bundesliga 2).
"They are a top team in the second division, and that's why they are not easy to play against. But we want to make it difficult for them too.
"This time we are the favourites, but in the cup, that's not that important. I'm looking forward to the game. It's an attractive draw. A difficult, but attractive one. It's all good."
Wolfsburg and Mainz were both drawn at home to second tier opposition - Aalen and Koln respectively - while last term's runners-up Stuttgart travel to Freiburg, who are yet to win in the top flight this season.
Schalke will visit Liga 3 outfit Darmstadt on Wednesday, while the Bundesliga's bottom club, Eintracht Braunschweig, who have just one point from six games, will look to take solace in the cup as they entertain Bochum.
Hoffenheim, who have made an indifferent start to their Bundesliga campaign, host second-tier strugglers Energie Cottbus, and there is an all-Bundesliga 2 clash on Wednesday when Frankfurt take on the division's bottom club Ingolstadt at home.
