Daniel Brosinski tried his luck before half-time and his shot took a deflection off Freiburg defender Marc Oliver Kempf's hand.
Mainz and Freiburg are 15th and 16th in the table respectively so the decision carried added weight in a relegation six-pointer.
Winkmann then blew for the break, allowing the players to go in for half-time - only for the VAR official to give the handball and award a penalty.
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Mainz remained the stronger team in the second half, and De Blasis wrapped up victory 11 minutes from time after an embarrassing error from Alexander Schwolow.
Both sets of players had already left the pitch for the interval when the technology flagged up a handball at the end of the first period, reports Guardian football journalist Andy Brassell on social media.
"We're not going out", said Streich as he led his confused players back into the changing room.
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The Freiburg keeper gifted Mainz possession inside his own penalty area, and Colin Quaison squared the ball to provide De Blasis with an open goal.
Mainz midfielder Pablo de Blasis scored the penalty to put the hosts 1-0 up. Protests have taken place during most Monday games.
The game kicked off and, for 45 minutes, not a great deal happened.
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Maybe also City will invest massively and they don't let the others close the gap to them, I don't know. He said: "Paul Tierney was unlucky in one decision but I don't blame him at all - it's football ".
The game also had to be delayed at the start of both halves as fans protested against the match being played on a Monday night.