Bayern disposed of Bayer Leverkusen on Wednesday and they were joined in the final by the Bundesliga champions after they beat VfB 2-0.
Croatian striker Ivan Klasnic netted the opener, with Nelson Valdez adding the second, and they could even afford to miss a penalty as Timo Hildebrand saved from Valerien Ismael.
The final takes place in Mainz on Monday, while the Bundesliga is set to kick off on August 6.