Henrikh Mkhitaryan struck in the first half for die Schwarzgelben, with Marco Reus and Jonas Hofmann both adding goals after the break, as the visiting side took a 3-0 win at the Allianz Arena.
Bayern has now picked up only a single point in the three top-flight games played since securing the Bundesliga title at Hertha Berlin last month and Guardiola admitted that the team is suffering a decided dip in form.
"Congratulations to Borussia Dortmund but during the first half we didn't find our game," the 43-year-old was quoted by TZ. "And during the second half we also lost something. We have up to now been a very good team defensively and we have not shown that today.
"It may be that I have made a mistake, that it was a mistake not to continue as we have been. But I will not take squad rotation as an excuse."
The Bavarians still have the chance to repeat the treble-winning success of last season, with a DFB-Pokal and Champions League semifinals against Kaiserslauten and Real Madrid respectively to look forward to, and sporting director Matthias Sammer played down the defeat.
"We had a bit of trouble with the rhythm, with the build-up play and have never made the right decisions," he said. "But it's no big deal. We were not concentrated enough at key stages and let Dortmund in. If two, three percent is missing from our ideas, then it is not enough in the Bundesliga.
"But our players are not robots and have feelings too."