Schalke, who visit holders Inter Milan in the Champions League quarter-finals first leg next week, were leading 2-0 with goals from Raul and Julian Draxler when German referee Deniz Aytekin ordered the teams off the pitchv for good.
"It is always sad when a game is stopped," Aytekin told reporters. "But even in the first half the assistants had been hit by lighters and coins."
He said it was now up to the German football federation (DFB) and its sports courts to decide on the matter in the coming days with Schalke possibly being awarded the win.
Schalke had 33 points and were in 10th place before the game while St Pauli are stuck in the relegation play-off spot.
The linesman was hit by a cup thrown from the stands minutes after Schalke grabbed their second goal and St Pauli saw two of their players sent off within 10 minutes of each other.
Raul, 33, had scored with a glancing header in the first half and 17-year-old Julian Draxler added another from close range midway through the second period.
"We cannot be punished for this tonight. We were 2-0 up just before the end," said Schalke sports director Horst Heldt.
Tempers flared late in the game and relegation-threatened St Pauli had Jan-Philipp Kalla and Fin Bartels sent off for harsh fouls on Peruvian Jefferson Farfan before anger boiled over in the stands and the linesman was struck on the back of the head.
"Such scenes are unacceptable. These things should not happen in stadiums. I can only apologise to the assistant in the name of St Pauli," St Pauli coach Holger Stanislawski told reporters.
