Xherdan Shaqiri looked to have given the treble-winners a narrow victory but a late strike from Nicolas Hofler meant the Bavarians had to settle for a point.
Xherdan Shaqiri put the visitors ahead after 32 minutes when he fired past Oliver Baumann in the Freiburg goal, but Bayern was pegged back five minutes from stoppage time when it conceded only the club's second goal of the season, as substitute Nicolas Hofler volleyed home from close range.
Guardiola made six changes to his side from the 2-0 win over Nurnberg ahead of Friday's UEFA Super Cup clash with Chelsea, with the likes of Franck Ribery, Arjen Robben and Mario Mandzukic all dropping to the bench.
The hosts were without the suspended Francis Coquelin, while Christian Gunter replaced Mensur Mudzja.
It was Freiburg which had the first goalscoring chance of the match when Julian Schuster's powerful strike forced a good save from Manuel Neuer after 11 minutes.
Soon after, Bayern’s Toni Kroos and Xherdan Shaqiri both stung the palms of Baumann during what was an entertaining opening period.
Guardiola’s much-changed side then began to control proceedings and was rewarded just after the half-hour mark when Shaqiri gave it the lead.
The Switzerland international controlled a Thomas Muller cross from the right, which evaded Oliver Sorg, and drove home past Baumann.
Despite dominating possession for the remainder of the half, the champions could not add to their slender lead before the break.
Shaqiri then almost doubled his tally for the game 10 minutes into the second period, forcing Baumann into a save with his feet, before Charles Laprevotte cut in from the left and hit the post with a curling effort for the home side.
With the game finely poised, Bayern should have doubled its lead when Kroos found himself clean through. However, the Germany international was thwarted one-on-one before the goalkeeper reacted well to deny Muller's follow up.
But, with just five minutes to go, the home side drew level, with substitute Hofler firing a left-foot volley past Neuer from close range.
Dante almost restored Bayern's lead three minutes later when he poked over from inside the six-yard box, but Guardiola was forced to settle for a share of the spoils for the first time this season.