PAOK thought it had secured a last-gasp win with an 89th-minute effort, only for the referee to alter his decision after the protestations of AEK players.
The goal was ultimately disallowed, meaning PAOK was unable to usurp its rival at the top of the table.
That sparked angry scenes in the stands and numerous people entered the pitch, including PAOK owner Ivan Savvidis and his security detail.
Savvidis, who appeared to usher his players off the pitch, confronted referee Giorgios Kominis and was then led away by his security.
He then had to be restrained as he appeared to aim some angry words towards one of the match officials.
The match was postponed after the referee went down the tunnel.
Although the officials re-emerged later, PAOK claimed on Twitter the game "was finally halted with the score 1-0" in favour of the home side, despite the late goal initially seeming to be disallowed.
AEK coach Manolo Jimenez appeared to confirm PAOK had been handed the 1-0 win, while the former Sevilla boss also heard claims Savvidis entered the pitch armed with a gun.
"Right now we are leaving the stadium escorted by the police," Jimenez is quoted as saying by Onda Cero.
"The referee has invalidated the goal of PAOK for offside, there was a brawl of players and many people entered the field, including their president with bodyguards.
"After the invasion, the referee has gone inside and after two hours wanted to resume. We said no. The shame is that in the end the referee has given them the goal, after all that has happened.
"We learned later that the president had a gun, we did not see it there on the pitch."
It is the second time in less than two months that PAOK's Toumba Stadium has been the setting of disturbances.
Earlier in the day, PAOK had a stadium ban and a three-point deduction revoked after an incident against Olympiacos on 25 February.
Olympiacos coach Oscar Garcia had been hit on the head by a roll of paper thrown from the stands, with his injury requiring a trip to hospital.