Two changes from Bayern from the league loss against Borussia Monchengladbach last Friday saw the return of Jerome Boateng and Kingsley Coman.
Freiburg were forced to make a change early in the match when an injury to Baptiste Santamaria resulted in the introduction of Amir Abrashi.
This gave the Bavarians stimulus to take the lead on seven minutes which Robert Lewandowski duly took when he sliced home a through ball from Thomas Muller.
Roland Sallai almost brought the visitors back level ten minutes later from a ball inside the six-yard area, but Bayern goalkeeper Manuel Neuer tipped the latter's shot for a corner-kick.
A injury enforced substitution happened on the side of the Bavarians too shortly before the half-hour mark, as Leroy Sane came on for Serge Gnabry who couldn't carry on playing following a knock.
Lewandowski should've bagged a brace 12 minutes in the second half following a close-range shot, but struck the crossbar before Florian Muller denied Leon Goretzka on the rebound.
Freiburg maintained positivity following 62 minutes and thus threw on a double substitution in Nils Petersen for Ermedin Demirovic and Lucas Holer for Sallai.
This reaped instant rewards when Petersen attacked a flick on to the back-post from Nicolas Hofler to bring the tie level with his first touch from the substitutes' bench.
However, the Bavarians regained the lead on 12 minutes thereafter when Muller charged down a knockdown from Sane to see his shot bounce off the ground and into the net.
Chances appeared for either side following the final seconds, but Lewandowski couldn't profit while the woodwork denied Petersen a second before Hofler dragged wide, as it finished 2-1.