The players had already gone to their changing rooms for the interval with the score at 0-0 when referee Guido Winkmann stopped his own descent down the tunnel after a message in his ear.
The start of the second half was also delayed by more than 10 minutes as fans twice threw toilet paper into one of the goalmouths.
"It leaves a bitter taste", Freiburg sporting director Jochen Saier said.
Super Eagles' defender, Leon Balogun was at his brilliant best for the second successive Bundesliga match as he inspired his team to a 2-0 win over Freiburg on Monday night, a result that sees Mainz 05 momentarily climb out of the relegation zone, AOIFootball.com reports.
The Freiburg keeper gifted Mainz possession inside his own penalty area and Colin Quaison squared the ball to provide De Blasis with an open goal.
As the players departed the pitch, Winkmann was told to consult VAR and ran over to the other side of the pitch to watch the replay on a monitor.
It came just before the break when Pablo De Blasis converted from the penalty spot to give the hosts a halftime lead - but that was only half the story. The Mainz forward then picked out his teammate De Blasis who slotted home - luckily off the post.
The ref maybe shouldn't have sent them off as quickly, it depends on how quickly VAR contacted him.
The VAR system has been used in the Bundesliga this season but not without controversy as it has been at the centre of several disputed decisions.