The German league game between St Pauli and Schalke on Friday was halted in the 88th-minute after a linesman was hit by a plastic cup full of beer.
Schalke were 2-0 up in the Bundesliga match after goals from Raul and Julian Draxler when referee Deniz Aytekin ordered the teams off the pitch.
Hosts St Pauli had two players sent off before the cup was thrown.
"Even in the first half the assistants had been hit by lighters and coins," said Aytekin.
It is now up to the German football federation and its sports courts to decide on the matter, with Schalke possibly being awarded the win.
Champions League quarter-finalists Schalke are 10th in the table with 33 points while St Pauli are in the relegation play-off spot.
"We cannot be punished for this. We were 2-0 up just before the end," said Schalke sports director Horst Heldt.
St Pauli coach Holger Stanislawski was quick to apologise to assistant referee Thorsten Schiffner, who was struck by the cup.
"Such scenes are unacceptable. These things should not happen in stadiums. I can only apologise to the assistant in the name of St Pauli," said Stanislawski.
