Xherdan Shaqiri scored the only goal in the 15th minute as Bayern collected their 14th straight victory.
Freiburg suffered their second straight defeat to remain on 45 points, albeit still well in the mix for the European berths inside the top six.
Bayern coach Jupp Heynckes made sweeping changes to his line-up, with Jerome Boateng the only starter remaining from the 4-0 demolition of Barcelona in the Champions League.
With so many changes, Bayern struggled to come up with many chances in the early going.
They went close after 20 minutes but Shaqiri's shot from Mario Mandzukic lay off went wide of the goal.
The Swiss midfielder did give Bayern the lead 15 minutes later, however, as his free-kick from the right side of the are flashed past Freiburg goalkeeper Oliver Baumann.
Bayern remained the dominant team but did not invest much effort in attack, although Mandzukic's looping shot over Baumann glanced off the crossbar in the 58th minute.
Heynckes decided to add some offensive firepower in the 74th minute, bringing on Mario Gomez and Franck Ribery.
And Gomez nearly made it 2-0 a minute later, heading wide of goal from a cross from Diego Contento, who was fed down the left side from Ribery.
The Ribery-Gomez connection almost netted a goal in the 85th minute but Gomez shot wide, before the striker missed another chance in the 88th minute from a tight angle.