A hat-trick from Thomas Muller set the Bavarians on their way, before substitute Xherdan Shaqiri came off the bench to cap off the win late on.
Despite his side rarely looking troubled, Guardiola conceded his team were off the pace during the opening stages at the Commerzbank Arena, although he was quick to praise their perseverance in front of goal.
He told reporters: "It's always difficult after a Champions League game. We struggled in the early stages.
"Going 3-0 up it became a different game. I'd like to congratulate my players."
The former Barcelona coach was also quick to praise opposite number Thomas Schaaf, who is beginning to feel the pressure after five straight defeats.
Guardiola added: "It's always hard to play against a team of Thomas Schaaf. They were very aggressive in defense and had a few problems with our setup."
The convincing win gives Bayern a seven-point lead at the top of the Bundesliga ahead of Wolfsburg's home clash with Hamburg on Sunday.
However, a determined Guardiola hinted that it would not be a time for his side to put their feet up ahead of the international break.
"We now have a few days to analyse our performances and find ways to improve," he added.