Robert Lewandowski continued his prolific form against his former employers with a brace, while Serge Gnabry was also on target before a Mats Hummels own goal completed the rout.
A close-season arrival from Bayer Leverkusen, Brandt found his first experience of the iconic Bundesliga fixture tough to take.
"It happens that we've lost. That's okay. But the way it happened was difficult for me," the forward said at a news conference ahead of Germany's concluding Euro 2020 qualifiers against Belarus and Northern Ireland.
"It's hard to digest it like that. For everyone it's okay to lose games. It's human. Every team is not perfect and that you have bad days is okay. But that wasn't so good."
Brandt saw attacking colleague Jadon Sancho hauled off before half-time for a sub-standard display and added: "We just weren't there that day. Everything was missing.
"The courage to go up front, the aggressiveness to go into the duels. If you don't have that in the end, then something like that happens."
Bayern's interim head coach Hansi Flick was the mastermind of Dortmund's downfall, taking charge of two matches heading into the international break after Niko Kovac's sacking.
Germany boss Joachim Low knows Flick well after he served as his assistant from his appointment in 2006 up to and including Die Mannschaft's 2014 World Cup triumph.
"I know Hansi by heart," Low said. "We worked together for eight years. The players also profited a lot from him.
"I talked to him on the phone last week. He was very calm and very balanced.
"Of course, Hansi has a clear idea of what he wants to convey to the team. So it was clear to me that he would have a good start.
"He has so much experience in so many areas. He has great competence and empathy. I believe Bayern will give him confidence."