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.
Both sets of players went down the tunnel, until the referee called them all back.
He ordered the players back onto the pitch much to the bemusement of Freiburg coach Christian Streich, who was seen shaking his head in disbelief. Some were looking at TVs to determine exactly what was going on.
Sussex weather forecast for the week ahead
Be sure to dress warmly out the door this Mid-April morning, and keep the warm clothes handy throughout the day today. We have a lull in showers now, but that will change as we head overnight as a strong cold front crosses the region.
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.
The confusion continued after the break, as fans threw toilet rolls onto the pitch in protest against Monday night games, delaying the restart by several minutes.
Mainz and Freiburg are 15th and 16th in the table respectively so the decision carried added weight in a relegation six-pointer. Protests have taken place during most Monday games. Wolfsburg is also under threat with four rounds remaining, while survival looks increasingly unlikely for Hamburger SV and Cologne, eight and nine points adrift of safety, respectively.