Mainz won the game 2-0.
Freiburg's players had already disappeared down the tunnel for half-time when referee Guido Winkmann referred a potential penalty to the video assistant referee.
Mainz initially had the penalty appeal turned down after right-back Daniel Brosinski's cross deflected off Freiburg centre-back Marc-Oliver Kempf's hand and was saved by keeper Alexander Schwolow.
A weird video assistant referee (VAR) decision caused mayhem in a Bundesliga game on Monday night when two teams were ordered back on to the pitch at half time because the referee chose to award a penalty after watching a replay on TV.
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Freiburg's players had to be summoned from the dressing room and back onto the pitch to allow the home side to take their penalty. He points to the spot after video review with Mainz eventually converting the penalty through Pablo de Blasis.
De Blasis added a second with ten minutes remaining, but there is likely to be significant fallout from this match (and that decision in particular) in the coming days.
"We thought that when the whistle goes for half-time, that the first 45 minutes are ticked off", Freiburg sporting director Jochen Saier told Eurosport. Protests have taken place during most Monday games.
After finally getting their half-time break, the players were forced to wait again for the second half after Mainz fans threw hundreds of rolls of toilet paper onto the pitch in protest against Monday night games.