Bayern dropped in a few changes from the thumping of Borussia Monchengladbach, with goalkeeper Alexander Nubel, Alphonso Davies, Leroy Sane and Serge Gnabry thrown in.
The Video Assistant Referee (VAR) was in the spotlight midway in the first half when it awarded Bayern a penalty following a foul on Thomas Muller by Lukas Kubler during a corner-kick.
Robert Lewandowski as such stepped up to do the honours to go equal with Gerd Muller's 40-goal a season record in the Bundesliga.
Freiburg needed just four minutes to pull themselves level when Manuel Gulde leaped at the end of a corner to head into the far side of Nubel's net.
The Bavarians did go on to reclaim the lead seven minutes in the second half after Sane reacted smartly to a first-time pass from Muller to tap into the net.
However, the lead was under threat again as Vincenzo Grifo fired a cutback from Christian Gunter after two minutes off against the side-netting.
Two substitutions from Hansi Flick followed on 62 minutes, with Marc Roca in for Lucas Hernandez before Muller shifted aside for French international Corentin Tolisso.
Freiburg had the champions on the edge in the last 20 minutes from two close-range efforts by Lucas Holer and Janik Haberer, however Nubel parried.
The host kept calm and levelled with ten minutes remaining after Gunter ran in from the left-side of the area to drill into the far corner.
Lewandowski was denied the landmark goal minutes later as goalkeeper Mark Flekken palmed his far post header for a corner shortly after making two point-blank saves.
The two sides went at each other for the ultimate winning strike before full-time, however it finished all square as Freiburg dropped to tenth spot.