Following a nervy first half Mainz took the lead in curious circumstances when they were given a penalty by Video Assistant Referee system VAR after the referee had already blown for half-time.
The players had just ventured down the tunnel and into their respective dressing rooms for half-time when the referee, Guido Winkmann, suddenly ordered them all back out onto the pitch.
Daniel Brosinski tried his luck before half-time and his shot took a deflection off Freiburg defender Marc Oliver Kempf's hand.
There were freakish scenes in the Bundesliga on Monday as Mainz and Freiburg players returned to the pitch so a penalty could be taken before half-time.
"We're not going out", Freiburg coach Christian Streich responded as he led his confused players back into the changing room.
Light Winds with Cool Temperatures for Monday
Tuesday night our temperatures will fall into the upper 20s to lower 30s with clouds mixing in with a bit of clear sky. Another chilly and wet weather system will be moving through the northern Rockies today and tomorrow.
And so, after a lengthy delay, the players returned and Pablo de Blasis opened the scoring for the hosts.
Mainz fans protest the Monday night contest by throwing toilet paper onto the field.
Finally, in the seventh minute of added time, De Blasis converted the penalty.
Mainz climbed to 15th on goal difference above Freiburg who fell to 16th, the relegation playoff spot.
Before the game began, both sets of fans waved signs reading "against Monday games" and a cocophony of whistles and vuvuzelas provided a constant soundtrack throughout the 90 minutes. I can't understand why referees are involved in the decision-making process at all, if it is to be used for clear and obvious errors, surely the VAR has to tell the referee what the decision is.