The Spaniard says he is not surprised his side have suffered a loss of form since retaining their league title
The champions have now taken just one point from three top-flight matches since retaining their crown at Hertha Berlin last month.
Guardiola's side had dropped just four points all season prior to their coronation in the capital, but drew 3-3 with Hoffenheim and lost 1-0 at Augsburg before this weekend's humbling at the hands of second-placed Dortmund.
"When you win the title, you suffer a dip," said the Spaniard.
"It was the same for me at Barcelona. Now we have to get back (to our previous form)."
Bayern were lacklustre throughout Saturday's contest, as Dortmund's front four of Pierre-Emerick Aubameyang, Henrikh Mkhitaryan, Marco Reus and Jonas Hofmann - Robert Lewandowski started on the bench - caused the back four all sorts of problems.
"Congratulations to Dortmund," Guardiola added.
"We didn't get into our rhythm today and we were unable to score."
Bayern goalkeeper Manuel Neuer was withdrawn at the break after complaining of discomfort in his calf, but the Germany number one was quick to insist he will be fit for Wednesday's DFB-Pokal semi-final against Kaiserslautern.
"I went off as a precaution but I can play in the cup in during the week," he said.