In the 45th minute, Freiburg's Marc-Oliver Kempf handled a shot from Daniel Brosinski in the six-yard box.
There were weird scenes in the Bundesliga on Monday as Mainz and Freiburg players returned to the pitch so a penalty could be taken before half-time.
Shortly before half-time there were muted appeals for a penalty decision, but they were turned down by referee Guido Winkmann.
He ordered the players back onto the pitch much to the bemusement of Freiburg coach Christian Streich, who was seen shaking his head in disbelief. Some were looking at TVs to determine exactly what was going on.
He ordered both sets of players back onto the pitch so that the penalty could be taken.
"It leaves a bitter taste, but we have to accept it with a heavy heart", Freiburg sporting director Jochen Saier told Eurosport at half-time. "Things are getting stranger". After the stewards cleared the paper strands, they threw another round they held back in reserve to delay the second half even further.
The Freiburg players were understandably outraged, in stark contrast to Mainz midfielder Pablo de Blasis who couldn't believe his luck as he gleefully stepped up and fired the ball into the bottom left corner of the goal, giving the hosts a 1-0 lead in the most bewildering of ways.
Protests also delayed the initial kickoff, and the whole game took place to the sound of shrill whistles as supporters made their displeasure known with the Bundesliga.
De Blasis scored a second on 78 minutes to secure victory, taking Mainz above Freiburg on goal difference and eight points clear of automatic relegation, while putting the visitors into the relegation play-off spot in 16th.