Mainz and Freiburg are 15th and 16th in the table respectively so the decision carried added weight in a relegation six-pointer.
Winkmann overturned the decision and awarded the hosts a penalty before having to recall the entire Freiburg side and the handful of Mainz players who had left the pitch.
He ordered both sets of players back onto the pitch so that the penalty could be taken.
Kempf, who conceded the spot kick, was substituted at halftime.
Mainz initially had the penalty appeal turned down after right-back Daniel Brosinski's cross deflected off Freiburg centre-back Marc-Oliver Kempf's hand and was saved by keeper Alexander Schwolow.
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.
Footage from broadcaster Eurosport during the incident showed that players from both teams were already in their respective dressing rooms when Winkmann requested they return to the field. Mainz forward Pablo De Blasis duly converted, and the home side went back into the tunnel one goal to the good.
Many German fans have opposed the introduction of Monday games, saying matches should be played on the weekend when most supporters can attend.
It was so loud that Mainz coach Sandro Schwarz even said afterwards that it was distracting, while VAR project leader Lutz Michael Fröhlich even suggested the noise had hampered the referee's ability to hear the video assistant on the crucial penalty call.
There was a further 10-minute delay before the start of the second half as fans threw hundreds of toilet rolls onto the pitch in a protest against Monday evening matches.
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