Proceedings were initially interrupted after just five minutes, as a section of the home support approached the Olympiakos bench, before security managed to calm the fracas.
Thrylos remained focused enough to take the lead through Miguel Angel Guerrero in the 53rd minute.
Local fans subsequently clashed with police, forcing them to use tear gas which made its way on to the pitch, resulting in German referee Marco Fritz calling a premature end to proceedings with 70 minutes played.
Away fans are banned from attending matches in Greece due to potential crowd trouble, but there was still evidence of Olympiakos banners in the OAKA stadium, with the home fans setting the flags on fire.
Olympiakos midfielder Kostas Fortounis rued the sorry situation.
"It's tragic, I cannot explain it," he told the club's official website.
"Getting into the stadium, chasing the players, our agents... I have no words. After the goal we put in, the fans came on the pitch.
"We could not continue the game. The players of Panathinaikos went to calm them, but they [the fans] were not [calm]."
Panathinaikos subsequently released a statement "condemning unequivocally every act of violence that took place".