Referee Guido Winkmann blew his whistle to signal the end of the opening 45 minutes of the match, with players from both sides leaving the pitch for the interval.
But a VAR intervention saw Winkmann call the players back from the dressing rooms after a handball by Freiburg defender Marc-Oliver Kempf was spotted on video replays.
After a lengthy delay, Pablo De Blasis stepped up to take the spot-kick for Mainz, beating Alexander Schwolow in the seventh minute of stoppage time to open the scoring for his side.
Supporters also forced the game to be paused by throwing rolls of toilet paper on to the pitch as a protest against the Bundesliga's introduction of matches on Monday nights.
Premier League clubs have voted against introducing VAR technology for next season, preferring to continue with tests.