With 15 minutes remaining and Bayern dominating possession but failing to carve out clear chances, Musiala dribbled past at least three Freiburg defenders and blasted a low shot into the right corner.
Bayern Munich were held to a 2-2 draw at Freiburg on Friday, an 87th-minute equaliser from Lucas Hoeler giving leaders Bayer Leverkusen a chance to go 10 points clear.
Mathys Tel’s 35th-minute stunner had cancelled out an impressive opener from Freiburg captain Christian Guenter, before Jamal Musiala’s spectacular solo effort looked to have snared the three points for Bayern.
Hoeler however had other ideas, chipping a volley through a crowded Bayern penalty area and past a helpless Manuel Neuer.
Bayern have now failed to win away from home in four matches dating back to January in both the league and Champions League.
Xabi Alonso’s Bayer Leverkusen can go 10 points clear of the Bavarians with a win against lowly Cologne on Sunday.
Guenter blasted the hosts into the lead after 12 minutes, unleashing a spinning rocket from outside the box and into the bottom right of the goal.
The goal was the Freiburg captain’s first of the season and the club’s only strike from outside the box this campaign.
Not content to allow Guenter to dominate the highlights reel, Tel hit back with a dream goal of his own, curling in a long-range effort on his second league start this season.
With 15 minutes remaining and Bayern dominating possession but failing to carve out clear chances, Musiala dribbled past at least three Freiburg defenders and blasted a low shot into the right corner.
Despite holding the lead Bayern grew passive, dropping deep to defend their goal and hold onto their slender lead.
With just three minutes of regular time remaining, Hoeler held off several Bayern defenders and chipped a volley over Neuer and into the goal, sending the home side into raptures.
The draw spoilt the first day at work for Bayern sporting director Max Eberl, who said during his unveiling this week the side would still push Leverkusen for the title.
The point sees Freiburg finish the night in ninth place in a crowded Bundesliga table, with only five points separating seventh and 15th places.