The Spaniard lost his first competitive fixture in charge of Bayern Munich since taking over from Jupp Heynckes, but insists there were positives to be drawn from the performance
The Bavarians had showcased impressive form coming into the encounter, but were outplayed at Signal Iduna Park as Jurgen Klopp's men dominated proceedings.
However, Guardiola has insisted there is no reason to worry and says he saw promise from his team despite blunders from defender Daniel Van Buyten and goalkeeper Tom Starke.
"They won. I am not here to analyse which team played better today. I am happy with our performance, we played well," the 42-year-old told reporters after the match.
"Congratulations to Dortmund, they won. We did not lose because of that [Van Buyten's and Starke's mistakes]. This is football. We have one week until the cup and another week to the Bundesliga.
"They won 4-2, but I did not have the feeling they were much better than us. But this is football. We will watch the match and work."
Captain Philipp Lahm bemoaned bad luck in the defeat, but reiterated die Roten would work at getting back to their best.
"This is not good, but it is not that bad either," he added.
"We wanted to win this match, but we did not score at the right times and conceded at the worst times possible. We have to analyse and then we will keep working."
Bayern's next competitive match is against BSV Schwarz-Weiss Rehden in the DFB-Pokal before hosting Borussia Monchengladbach in their opening Bundesliga fixture.