Hertha did not just pack men behind the ball at the Allianz Arena, as opponents of Bayern often do, but instead created chances and attacked, taking the lead and going close to equalising late on.
"They are the best team we have played against so far this season," Guardiola said at the post-match press conference. "We were not very good today."
The Catalan was relieved with the result, and even more pleased that his players now have a full week off to look forward to after a hectic recent schedule.
"The players need this time," he said. "We've got all week to recover for our next game in Hoffenheim.
"We've had lots of games in the past two months and we're a bit tired, and you could see that today."
Hertha coach Jos Luhukay felt his team had been unfortunate not to become the first side to take points off Bayern at the Allianz Arena.
"All that was lacking was a tiny bit of luck. Otherwise we would maybe have taken a point away," he said.
"Congratulations to Pep and his team. The substitutions saw us lose our self-assurance, and that's when the equaliser came."
Those injury-enforced changes of Toni Kroos and Arjen Robben in quick succession were not as worrying as first thought, however, with Guardiola putting both down to the busy programme.
"They've played lots and lots of games lately and these things happen," he said.
Robben said his injury was "not so bad - it's probably just a nerve", while Kroos also expects to be fit next weekend.