The Bavarians kicked off their cup defence with a 4-1 first-round victory at Preussen Munster but they could have a far tougher time of it at the Imtech Arena
Pep Guardiola's side were not rewarded with a kind draw after defeating Preussen Munster 4-1 in the opening round.
They will face their Bundesliga rivals next up away from home, although Mirko Slomka's men were less than convincing in their first-round clash with Energie Cottbus, only progressing on penalties after a 2-2 draw.
Bayern kicked off their Bundesliga title defence with a 2-1 win over Wolfsburg on Friday, while Hamburg held Cologne to a goalless draw a day later.
In the other standout tie of the round, Eintracht Frankfurt were pitted against Borussia Monchengladbach, while amateurs Magdeburg have been rewarded for their shock 1-0 win over Augsburg with the chance to host Champions League hopefuls Bayer Leverkusen.
Borussia Dortmund visit St Pauli in one of five matches between teams from the first and second tiers, with 1860 Munich's clash against Freiburg one of the other notable matches.
Dynamo Dresden of 3. Liga ousted Schalke in the first round and host fellow giant-killers Bochum, who disposed of Stuttgart.