Jupp Heynckes' men looked horribly out of sorts in Berlin, suffering a fifth successive defeat at the hands of their great rivals in all competitions after Robert Lewandowski netted a hat-trick following earlier strikes from Shinji Kagawa and Mats Hummels.
While Germany boss Low felt that Bayern got what they deserved, he does not believe that their hopes of claiming a fifth European Cup title will have have been affected by what happened at the Olympiastadion.
“I never expected this result," the 52-year-old coach told reporters after the game. "But especially based on the second half it's a deserved victory.
"Dortmund always show plenty of bite against Bayern, but I think we'll see a huge reaction from Bayern against Chelsea next weekend."
The Bavarians will tackle the Blues in their own Allianz Arena next Saturday evening, with the eagerly-awaited encounter scheduled to kick off at 20.45CET.