Dortmund led 1-0 and 2-1 in regulation but Bayern equalized on an own goal in the 88th minute. Dortmund led into the fourth round of the shootout that followed the 90 minutes but missed two of its final three penalties.
"If you're 2-1 up with two minutes remaining, then you have to win the match," said new Dortmund coach Peter Bosz. "But we didn't. We were in the lead on three occasions if you include the penalty shootout. That's why we're disappointed."
Aug. 5 in Dortmund
Bor. Dortmund 2 Bayern Munich 2. Goals: Pulisic 12, Aubameyang 71; Lewandowski 18, own goal 88.
Bor. Dortmund -- Buerki; Piszczek, Bartra, Sokratis, Zagadou (Passlack 77); Sahin, Castro, Dahoud (Rode 46); Dembele, Pulisic (Philipp 90), Aubameyang.
Bayern Munich -- Ulreich; Rafinha, Hummels, Martinez (Suele 60), Kimmich; Vidal, Rudy, Tolisso (Sanches 84); Mueller (Coman 67), Ribery, Lewandowski.