In the dying seconds of the first half, Mainz had an appeal for handball turned down by referee Guido Winkmann, with the scores still at 0-0.
The win saw Mainz move out of the bottom three for the first time since January, drawing level on points with Freiburg, who drop down into the relegation play-off place.
De Blasis later doubled the home side's lead in the 79th minute and the game finshed 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 (VAR).
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"We were under the impression that when the referee blows for half-time that's it", said Saier.
There were shambolic scenes im the Bundesliga last night when VAR once again reared its ugly head to disrupt the match between relegation-threatened Mainz and Freiburg at the Opel Arena.
This is the latest VAR-related controversy in a long line of decisions involving the technology.
Many German fans have opposed the introduction of Monday games, saying matches should be played on the weekend when most supporters can attend.
Premier League clubs have voted against introducing VAR technology for next season, preferring to continue with tests.