Dante put Pep Guardiola's men in front in the 19th minute before two deflected goals from Xherdan Shaqiri sealed victory before half time.
Guardiola made changes in the second half, giving the likes of Philipp Lahm and Arjen Robben a break and introducing Bastian Schweinsteiger before Claudio Pizarro sealed victory late on, keeping them on course for the Bundesliga title.
Freiburg made a bright start, following the example set by Nurnberg last weekend in trying to attack the Bavarians rather than sitting back and accepting defeat.
Their good intentions did not last for long, though, as Diego Contento lifted the ball in for Dante to flick his header past Oliver Baumann, who was unable to keep the ball out with his fingertips.
Swiss midfielder Shaqiri made it two when he broke into the penalty area from the left and his diagonal shot took a telling deflection off Oliver Sorg to take it in off Baumann's inside post.
Robben nearly made it three in fine style in the 38th minute, but having seemingly done the hard work in dribbling past three Freiburg defenders, he lifted his shot over the crossbar.
It did not matter too much, though, since Shaqiri put the result beyond doubt in the 42nd minute when he turned Toni Kroos' cross in with the help of a deflection off Thomas Muller.
Admir Mehmedi thought he had pulled a goal back, but the offside flag was wrongly raised to deny him in the 43rd minute.
Sebastian Kerk pulled a shot wide of the far post midway through the second half, but Bayern's lead was never in danger and Guardiola started to make the changes in view of Wednesday's trip to London.
It did not weaken his side in any way and Javi Martinez missed the chance to get his name on the scoresheet before Pizarro showed him how it should be done two minutes from time to complete the rout.