Claudio Pizarro came off the bench at the Allianz Arena on Saturday to net a stoppage-time winner with the last kick of the game as Bayern finished the season 19 points clear of second-placed Borussia Dortmund.
Bayern will have concerns over Bastian Schweinsteiger and Mario Mandzukic, both of whom limped off during the victory, especially with a DFB-Pokal final against Dortmund to come next weekend.
Immediately after the game, however, Guardiola was in celebratory mood, having been showered in beer and having dropped the trophy in the aftermath of Bayern's on-pitch presentation.
"I'm very proud of this team and these players," he told reporters.
"[The beer] is cold! It's all okay now after having a proper shower. I'm happy!"
On Schweinsteiger, Guardiola remained positive and hopes the Germany midfielder will be fit for next Saturday's clash in Berlin.
He added: "Bastian had problems with his patella tendon but we still have six days [before the cup final]."