Ousmane Dembele's 74th-minute winner clinched a 3-2 victory over Bayern for eventual Pokal champion Dortmund back in April and Jupp Heynckes' side will be out for revenge when the two teams meet at Signal Iduna Park in December.
The draw means that Bayern will travel to Dortmund twice in the space of six weeks, given the Bundesliga fixture scheduled for 5 November, and as it stands it is only three points between them at the top of the table.
Other stand-out ties in the DFB-Pokal include Bayer Leverkusen travelling to Borussia Monchengladbach and Schalke entertaining Cologne.
Werder Bremen have been drawn against Freiburg, Mainz will take on Stuttgart, and Wolfsburg travel to Nuremburg.
The remaining ties see Paderborn at home to Ingolstadt, while Heidenheim will play Eintracht Frankfurt.
DFB-POKAL LAST 16 DRAW:
Mainz v Stuttgart
Nurnberg v Wolfsburg
Bayern Munich v Borussia Dortmund
Heidenheim v Eintracht Frankfurt
Werder Bremen v Freiburg
Borussia Monchengladbach v Bayer Leverkusen
Paderborn v Ingolstadt
Schalke v Koln