The manager is pleased that his players now have a week off so they can recuperate ahead of their next fixture.
The capital club had surged into an early lead before Mario Mandzukic, who struck twice, and Mario Gotze responded for the treble winners, although Anis Ben-Hatira then set up a nervy finish for the Bavarians after the break.
Guardiola attributed Bayern's tough outing to his men being down to their last legs after the recent slew of international and European fixures.
"We weren’t very good today," the 42-year-old coach told reporters after the match. "In the coming week, we have time to regenerate and prepare for the trip to Hoffenheim. My players need the time. We’ve played a lot of matches in the last two months and they’re a little tired, as we all saw today.“
Captain Philipp Lahm echoed his coach's sentiments, explaining the prolonged stretch of games had taken its toll on the Bavarians' performances.
"You could see we were weary, mentally as well as physically. But in this situation, the important thing is to take the three points," the Germany international said. "We’re looking forward to the normal week coming up now. It’s been a packed programme, especially for the internationals. We’ve changed a lot of things around, which requires plenty of concentration and alertness, but it gets to you. It’s good we can clear our heads now.“
Despite its packed schedule, Bayern has surged to the top of the Bundesliga and sits a point clear of closest rival Borussia Dortmund.