Mainz and Freiburg are 15th and 16th in the table respectively so the decision carried added weight in a relegation six-pointer.
Referee Guido Winkmann initially allowed the game to play on, denying Mainz a penalty, before blowing for halftime shortly thereafter.
Mainz have benefited from a freaky penalty decision which helped to seal a controversial 2-0 victory over fellow strugglers Freiburg in the Bundesliga.
Daniel Brosinski tried his luck before half-time and his shot took a deflection off Freiburg defender Marc Oliver Kempf's hand.
Mainz midfielder Pablo de Blasis scored the penalty to put the hosts 1-0 up.
Then the second half was delayed because fans hurled an avalanche of toilet rolls onto the pitch, in protest of the Monday night kick-off.
By this point players from both sides had walked down the tunnel for the interval before Winkmann changed his decision and recalled the teams so Mainz could take their spot kick.
De Blasis followed the penalty, officially recorded in the seventh minute of first-half stoppage time, with a second goal in the 78th minute to seal the win.
Potentially one of the most vital goals in the fight at the bottom, but a new low for VAR.
In this case you've got a couple thousand fans off to the bar and they come back thinking it is 0-0.