The Bundesliga game between St. Pauli and Schalke was called off in the 88th minute Friday after a fan threw a plastic glass full of beer at a linesman.
"We had to call off the game. There was no other choice," Aytekin said.
He pointed out that coins and lighters had also been thrown at Schiffner, who had to be examined by a doctor.
"That's totally unacceptable. It's not tolerated. I can only apologize to the linesman," St. Pauli coach Holger Stanislawski said.
Aytekin suggested the linesman was "doing as well as can be expected under the circumstances."
There was no immediate decision from league officials about whether the result would stand.
"It casts us in a very bad light," St. Pauli goalkeeper Benedikt Pliquett said.
Raul Gonzalez had given the visitors the lead in the 26th minute and substitute Julian Draxler added the second in the 66th, in coach Ralf Rangnick's first game in charge since returning to the club after Felix Magath was fired.
The game turned ill-tempered as St. Pauli was reduced to nine men after Jan-Philipp Kalla was given a second yellow card in the 68th and teammate Fin Bartels earned a direct red for a wild challenge on Farfan in the 79th.
Raul had almost given the visitors a perfect start when he hit the post in the second minute, before Schalke had a penalty appeal waved away when Alexander Baumjohann fell under the challenge of Fabian Boll.
The visitors were still protesting when Gerald Asamoah - a former Schalke player - whipped in a dangerous cross that Charles Takyi just missed.
Farfan almost opened the scoring in the 23rd, when Pliquett blocked his shot from a narrow angle.
The goalkeeper saved from substitute Edu a minute later, but Raul scored from the resulting corner when he ran into space to glance Farfan's cross beyond Pliquett.
It was the Spaniard's 12th goal of the season.
Fin Bartels flashed a shot narrowly over in a rare St. Pauli attack, before Markus Thorandt's crucial interception prevented Schalke going further ahead in the 38th as the visitors dominated possession.
Raul's audacious chip from near the halfway line landed on the roof of the net before halftime, and the Spaniard almost created another goal immediately after the restart, before the ball was eventually cleared away.
St. Pauli, playing with increased urgency, was much improved, and had a penalty appeal of its own turned down when Rouwen Hennings was brushed off by Kyriakos Papadopoulos.
Manuel Neuer, playing in his 150th Bundesliga game, was first called to action in the 55th, when he easily gathered Takyi's shot.
St. Pauli had a goal ruled out in the 65th, when Boll was adjudged to have been offside despite failing to connect with Max Kruse's free kick that ended in the net.
The home side's protests had not died down when Draxler scored at the other end, the 17-year-old prodding in Farfan's cross from close range.
It went from bad to worse for St. Pauli with the sendings off of Kalla and Bartels, before the game was halted.
"It's a bad day for St. Pauli. We have to launch an inquiry," St. Pauli sport director Helmut Schulte said.