The players had just ventured down the tunnel and into their respective dressing rooms for half-time when the referee, Guido Winkmann, suddenly ordered them all back out onto the pitch.
Mainz were rewarded with a penalty when the players had already left the pitch for half-time.
Pablo de Blasis scored one of the most remarkable goals in Bundesliga history - during the halftime break - as Mainz beat relegation rival Freiburg 2-0 amid fresh protests against Monday night games.
Speaking to Eurosport at half-time, Jochen Saier said: "It leaves a bitter taste".
Kleindienst, on as a half-time substitute, almost equalised with a header at the right end moments later but the visitors were made to pay in the 78th minute.
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A mistake from Schwolow in the final minutes allowed De Blasis to seal the home side's first win since January. Die Breisgauer have dropped into the relegation play-off spot - 16th - due to their inferior goal difference.
"But for us who try to attend every game in the stadium it's quite hard to travel on Monday to a match".
He added: 'We were under the impression that when the referee blows for half-time that's it'.
The second half was then delayed by fans throwing toilet paper onto the pitch, which was not related to the penalty decision but instead a protest against Bundesliga fixtures being played on Monday nights.
Premier League clubs have voted against introducing VAR technology for next season, preferring to continue with tests. I can't understand why referees are involved in the decision-making process at all, if it is to be used for clear and obvious errors, surely the VAR has to tell the referee what the decision is.