Referee Guido Winkmann, who had also been on his way to the tunnel, ordered the players to come back so that Mainz's Pablo De Blasis could take the spot-kick, which he duly converted.
The Freiburg team eventually emerged back onto the pitch, where Winkmann explained to a bemused Streich that it was a penalty for the home side.
VAR confusion reigned in the Bundesliga on Monday evening as Mainz and Freiburg players had to be recalled from the half-time break after a penalty was belatedly awarded.
The curse of VAR struck again as chaos descended during Mainz's game against Freiburg in the Bundesliga.
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.
The penalty was given for a handball by Marc-Oliver Kempf that the VAR noticed after the halftime whistle had blown.
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"We're not going out", said Streich as he led his confused players back into the changing room.
De Blasis added a lucky second as his shot rolled over the line after hitting the inside of the post, with Schwolow out of his goal having passed the ball straight to Mainz midfielder Robin Quaison.
Many German fans have opposed the introduction of Monday games, saying matches should be played on the weekend when most supporters can attend.
Mainz fans protest the Monday night contest by throwing toilet paper onto the field.
"We thought that when the whistle goes for half-time, that the first 45 minutes are ticked off", Freiburg sporting director Jochen Saier told Eurosport.