A 4-2 victory for the Westphalians ended Bayern's recent dominance of German football and denied them the chance of winning six trophies in 2013, much to the delight of their coach Jurgen Klopp.
"The cool thing about the Supercup is that the losers are not too bothered, but the winners are delighted, and we won it," he said.
"It was a great game. There are still two weeks to the start of the Bundesliga season and both sides gave it a go like there was no tomorrow."
Although victory will be a morale boost for Dortmund, Klopp insists the game will have no bearing on the upcoming Bundesliga season, which Bayern will still enter as overwhelming favourites.
"We have always said that if we meet Bayern we want to beat them, but we don't see them as our rivals," Klopp said on ZDF television.
"They are the best team in the league. Of course we want to beat them when we can, but the other 16 sides are our real rivals."
Bayern captain Philipp Lahm played down his side's first defeat since losing to Bayer Leverkusen in the Bundesliga last October.
"It's still only pre-season," he said. "Of course we'd have liked to have won and we had chances to do so.
"We could have made it 3-3 but we didn't score at the right time while we conceded at the worst time.
"Last year, it was different. We had not beaten Dortmund for a while so beating them was good for our self-confidence.
"Now we've got to analyse this and move on. We work very hard every day and I think things still look very good for us."
Arjen Robben did not let the boos distract him as he scored twice for Bayern against the side his goal defeated in the Champions League final last May.
"Maybe they (the boos) do me good," said the Dutchman. "Clearly the Champions League still hurts them, but they can keep whistling me if I score the goals.
"I think the most important thing for us was that we fought back into the game, but when they made it 3-1 in just a few minutes the game was almost over.
"We fought back again, but they landed the killer blow to make it 4-2."