Shortly before half-time there were muted appeals for a penalty decision, but they were turned down by referee Guido Winkmann.
During the game, Mainz benefited from a weird penalty decision.
Mainz on Monday returned to winning ways and climbed off the relegation play-off spot after grabbing three vital points following a victory over struggling Freiburg, who suffered their fourth straight loss, reports Xinhua news agency.
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.
Mainz fans then delayed the second half by 10 minutes after throwing rolls of toilet paper onto the pitch in protest against Monday night matches. The sprinklers were on at the time he made the decision to call the visitors back onto the field in the Bundesliga fixture.
Speaking to Eurosport at half-time, Jochen Saier said: "It leaves a bitter taste".
When the game was eventually restarted Mainz doubled their lead in the 78th minute after a shocking error from the visiting keeper, who gifted the hoists the second and final goal of the game. Saier added: "We were under the impression that when the referee blows for half-time that's it".
As well as Germany, VAR technology has also been rolled out in Italy, Spain and the U.S., among other countries, each to varying degrees of success, but later this year it will be used on the biggest stage of all: the World Cup.