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 win saw Mainz move out of the bottom three for the first time since January, drawing level on points with Freiburg, who drop down into the relegation play-off place.
Daniel Brosinski tried his luck before half-time and his shot took a deflection off Freiburg defender Marc Oliver Kempf's hand.
But while the players were walking back down the tunnel towards the dressing room, the video assistant asked Winkmann to look at the penalty call again.
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.
SANA: Syrian air defenses repel strike on Shayrat air base in Homs
A local reporter for The Arab News said Israeli warplanes were spotted in Syrian airspace just before the missiles were reported. Up to 10 missiles were destroyed by the Syrian Armed Forces, a military source told Sputnik.
De Blasis added a second with ten minutes remaining, but there is likely to be significant fallout from this match (and that decision in particular) in the coming days. One Freiburg player could even be heard saying: "No, we're not coming back out".
So, about Mainz vs. Freiburg.
Before the game began, both sets of fans waved signs reading "against Monday games" and a cocophony of whistles and vuvuzelas provided a constant soundtrack throughout the 90 minutes.
The second half was delayed by fans throwing toilet paper onto the pitch.