Goals from Henrikh Mkhitaryan and Pierre-Emerick Aubameyang were enough for Dortmund as Guardiola juggled easing his key players back into action with trying to get one over their rivals.
Out of the seven Bayern stars involved in Germany's World Cup triumph, only Manuel Neuer, Thomas Muller and Jerome Boateng started on Wednesday, while Guardiola's opposite number Jurgen Klopp was without Mats Hummels and Marco Reus.
After the game Guardiola congratulated Dortmund and insisted his side will be much better by the time the Bundesliga kicks off, but revealed his main concern is now Javi Martinez after he had to be taken off before half-time.
"Congratulations to Jurgen Klopp and his team. We played well in the first 15 minutes but we had a few problems after that. We dropped too deep in the second half. We still need time," he told www.fcbayern.de.
"The worst news is the serious injury sustained by Javi Martinez, because he was in good form. We'll find out how bad it is on Thursday, but I think he'll be out for a long time."
Former Dortmund striker Robert Lewandowski, who was making his competitive bow for Bayern, conceded that his previous employers were the better team on the day.
He said: "It was the first match and pre-season has been tough. We wanted to win but BVB played the better football today. We need to turn our focus to the next match and I think it'll be a great deal better. I hope Javi's injury isn't serious."
While everyone at Bayern sweats on the fitness of Martinez, Klopp could not be happier with his side.
Following on from their dismal 4-0 friendly defeat to Liverpool last Sunday, Klopp demanded a reaction and he got one.
"Given the stage we're at that was a fantastic performance. We are certainly not the undeserved winner," he told www.bvb.de.
"It was also about reacting to what happened against Liverpool. That we did not like because it was the complete opposite of the way we want to play football. Today I was able to recognise our football."