The German champions made it 41 games unbeaten in the top flight thanks to goals from Mario Mandzukic, Mario Gotze and Xherdan Shaqiri at the Allianz Arena.
Bayern are guaranteed to lead the Bundesliga into the mid-season break but Guardiola believes his team were looking ahead to a potential fourth title of the year in Morocco, having only made the result safe in stoppage time after Pierre-Michel Lasogga pulled one back in the second half.
The Spaniard said: "Congratulations to Bayern for an incredible year.
"We had problems in the second half because we gave the ball away too easily. We must correct that.
"The players already had Marrakech in their heads. I will try to persuade them that we have much more work waiting for us.
"But after Champions League games, it is always difficult. Now we fly to Morocco, to win the last title this year."
Guardiola took the opportunity to rest the likes of Franck Ribery and David Alaba in the game, with the former coming on for the final 26 minutes.
Captain Philipp Lahm played the full match however, stating afterwards that his team-mates are not ready to rest on their laurels.
"We have already won four titles this year. But we are not finished yet," Bild quotes him as saying.
"We also want the Club World Cup."
