The build-up to the contest was dominated by the news that Bayern boss Vincent Kompany was taken to hospital after collapsing at the training ground on Friday.
The club subsequently confirmed that Kompany’s coaching staff will oversee first-team affairs while the Belgian gets the required time and support he needs to recover.
With Bayern looking to respond to Borussia Dortmund’s win over Frankfurt, Kompany’s assistant Aaron Danks could not have wished for a better start as Dayot Upamecano started and finished an incisive counter-attack to open the scoring in the 16th minute.
After blocking a shot on the edge of the box, Upamecano continued his run as the ball was worked out to Michael Olise, who sent the defender through on goal for a composed finish into the bottom corner.
Mio Backhaus prevented Nathaniel Brown from doubling the lead just after the half-hour mark, but he could do nothing to stop Serge Gnabry’s effort in the closing stages of the first period.
The attacker raced in behind to collect Brown’s through pass and kept his cool, slotting a low shot past the goalkeeper to send the visitors into the break with a healthy lead.
Searching for inspiration, Freiburg boss Julian Schuster made a double change just before the hour mark, including the introduction of Igor Matanovic, who threatened to make an immediate impact when his ambitious strike from distance forced Jonas Urbig into a rare stop.
Bayern’s goalkeeper was eventually beaten in the 82nd minute, when Tom Bischof inadvertently diverted the ball into his own net in his attempt to block a dangerous cross.
That effort set up a thrilling finish that saw Sacha Boey score a disallowed goal and Urbig pull off a superb reaction to stop Matthias Ginter’s header, shortly before Olise made sure of the result when he rolled a long-range shot into an empty net after Backhaus was caught in possession in no man’s land.
The victory ensures Bayern head into Der Klassiker above Dortmund on goal difference, while Freiburg are left four points adrift in fourth spot.
Flashscore Man of the Match: Michael Olise (Bayern Munich)