Savvidis, who was a sergeant major in the Soviet Army, was restrained by bodyguards as he came close to the referee.
PAOK chairman Savvidis was furious at the decision and invaded the pitch with his gun strapped on to his waistband.
PAOK hosted AEK on Sunday with the hopes of cutting their lead at the top to just two points but a Fernando Varela strike which would have been a let victor was ruled out for offside.
Greek-Russian businessman Ivan Savvidis asked his PAOK Salonika players to leave the pitch when a late goal was ruled out for offside, and then walked toward the referee while carrying what appeared to be a gun in a hip holster.
He was angry after his side had a 90th minute goal against rival club AEK Athens disallowed for offside.More news: England honeymoon over for Jones: Woodward
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AEK's Spanish coach Manolo Jimenez saw the firearm and claims to have heard Savvidis threatening the referee verbally. "We said no. The shame is that in the end the referee has given them the goal, after all that's happened". "There will be relevant announcements on the issue soon". Adding to the widespread confusion there were claims referee Giorgos Kominis had actually allowed the goal. Federation Internationale de Football Association also threatened to suspend the top Greek league over the government's intervention into a dispute with its referees (FIFA rules prohibit government interference of any kind).
The game was played less than 24 hours after PAOK had a points deduction overturned.
An official statement was expected from the league.
The match was minutes away from ending before Savvidis managed to get the game called off.