Fernando Varela broke the scoreless deadlock with a header in the 90th minute, putting the hosts on top, but the referee, who first signaled a score, then seemed to indicate an offside causing a frenzy in the stands.
The owner, Ivan Savvidis, invaded the pitch twice accompanied by bodyguards. On the second occasion, he took off his coat, revealing what appeared to be a pistol in a holster on his hip.
The match had to be suspended and was later declared a 0-0 tie, while referee Giorgios Kominis said the Greek-Russian businessman threatened him.
Kominis reportedly changed his decision to allow the goal for PAOK, and the league website currently has the result listed as a 1-0 win for the home team.
An arrest warrant has been issued on Savvidis, as well as four other people, but Skai TV reports it only concerns the pitch invasion itself.
The 59-year old reportedly does have a license; however, even police officers on duty are not allowed to carry firearms inside football stadiums in Greece.