The reigning Bundesliga champions secured a 3-0 victory at Signal Iduna Park on Saturday, extending their unbeaten league record to 38 matches.
It took Bayern 66 minutes to make the breakthrough with Mario Gotze coming off the bench to notch the opener against his former club.
Arjen Robben doubled the lead with a swift breakaway and sublime chip over Roman Weidenfeller, before Thomas Muller swept home a third to add gloss to the scoreboard.
And Guardiola was satisfied with the success, as Bayern's lead over Jurgen Klopp's outfit stretched to seven points, while Bayern re-established a four-point lead over second-placed Bayer Leverkusen.
"We are happy because we won against the best counter-attacking team in the world," he said.
"If we let them run, (Jakub) Blaszczykowski, (Marco) Reus and (Henrikh) Mkhitaryan they do not stop.
"We played well in the first 15 minutes, then for 30 minutes not so well. In the second half we played better again with Thiago (Alcantara), Mario Gotze, Toni Kroos and Philipp Lahm."
