PAOK president Ivan Savvidis entered the field with his security team to confront the referee after his side had an 89th-minute goal from Fernando Varela ruled out for offside with the score at 0-0.
Images taken on the pitch showed Savvidis apparently carrying a gun in a holster during the chaos that followed, with players and officials eventually leaving the field.
The match was abandoned two hours later and, although PAOK tweeted to claim a 1-0 win, the goalless draw was upheld, meaning the host remains five points shy of AEK in third and winless in its past three games.
When PAOK will have the opportunity to remedy that slump is now anyone's guess after Deputy Minister of Sport George Vassiliadis announced all matches would be suspended until further notice.
"We will not allow the phenomena of the past to be resurrected, assuming the political cost where necessary," he said after an emergency meeting with Prime Minister Alexis Tsipras, having pledged to make "bold decisions" on the matter.
"The most important thing is the rules that apply to everyone. We decided to discontinue the championship."
Controversy has marred Greek football over recent years.
Games were suspended in all divisions after referee's chief Giorgos Bikas was the victim of an arson attack in November 2016, while investigations into a match-fixing scandal that came to light in 2011 remain ongoing.
Two weeks ago, PAOK's home game with Olympiacos was abandoned before kick-off when visiting coach Oscar Garcia was struck by a roll of paper thrown from the stands. PAOK was initially docked three points but overturned the decision on appeal.
"For three years now, the government has fought to redeem path of football," Vassiliadis continued. "In the next few hours we will start meeting with the federation and the league.
"We are in open communication with UEFA and will not restart unless there is an agreed framework from everyone to move forward with terms and rules.
"We are continuing the battle for transparency and better football. Everything is on the table.
"We are waiting for the proposals from the federation and the league. We're on an indefinite interruption. We are expecting a new framework of rules."
UEFA and FIFA condemned the events at PAOK versus AEK but maintain any disciplinary measures to be imposed fall under the jurisdiction of the Greek Football Federation (HFF).