Munich are aiming for a milestone 20th cup title. PHOTO: AFP
Bayern, who are aiming for a milestone 20th cup title, were made to work hard by Schalke as the home team missed several chances either side of Joshua Kimmich's 40th-minute winner.
Schalke striker Guido Burgstaller hit the crossbar and then had a goal ruled out for a marginal offside before Kimmich volleyed home from the edge of the penalty area.
The home team's forward Rabbi Matondo missed a sitter with a feeble close-range shot in the 64th minute after a fast break and Bayern were forced to hang on in the closing stages as Schalke piled on the pressure.
Saarbrucken knocked out top-tier opponents Fortuna in the day's opening fixture as they won the penalty shootout 7-6, with the absorbing contest ending 1-1 after normal and extra time.
Goalkeeper Daniel Batz was Saarbrucken's hero as he saved five penalties, one in normal time and four in the shootout, to send his side through and spark wild celebrations among the jubilant home fans.
Midfielder Tobias Janicke fired Saarbrucken ahead in the 31st minute with a neat finish before Mathias Jorgensen levelled with a late header to force extra time after Batz had kept out a Rouwen Hennings penalty.
Fortuna missed two chances to win the shootout as Batz denied Kevin Stoger and Matthias Zimmermann and then saved Jorgensen's spot-kick after Janicke had drilled in Saarbrucken's final penalty.
In the other two quarter-finals, Bayer Leverkusen entertain Union Berlin and Eintracht Frankfurt are at home to Werder Bremen on Wednesday.
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