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.
The German football federation will launch an investigation into the matter. “We cannot tolerate such incidents,” said the federation’s chief executive Holger Hieronymus.
Schalke could be awarded the 2-0 win, while St Pauli face a fine and could also be ordered to play a home game without spectators.
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.
Police identified the fan who threw the cup and detained him, although he was not identified.