Gnabry, Müller save Bayern from German Cup upset in Bochum
An own goal from Canadian teen Alphonso Davies in the 36th minute had put the home side on course for a win over the defending champion.
"For 60 minutes we didn't play as we planned to do. Bochum were great," said Kovac, who criticized his side's mistakes. "The first half was a missed-pass festival."
Gnabry equalized with a volley in the 83rd and Müller grabbed the winner in the 89th after Armel Bella Kotchap had been sent off the minute before. The 17-year-old Bochum defender had had an excellent game, but attempted to make up for a mistake by bringing down Müller, who would have been through on goal.
Lewandowski went without scoring for the first time in a competitive game for Bayern this season.
Schalke survived a scare to win 3-2 at second division Arminia Bielefeld, which scored two late goals, struck the post and had the ball cleared off the line in a frenetic finale.
Bayer Leverkusen defeated Paderborn 1-0 and Karlsruher SC won 1-0 at second-division rival Darmstadt.
Also, fourth-tier side Saarbrücken scored late to upset Cologne 3-2, Union Berlin defeated Bundesliga rival Freiburg 3-1 away, Hoffenheim won 2-0 at third-division Duisburg, and Stuttgart needed extra time to beat second-division rival Hamburger SV 2-1.
Borussia Dortmund hosts Bundesliga leader Borussia Mönchengladbach in the pick of Wednesday's games.