PAOK president Ivan Savvidis has been banned from all football grounds for three years after storming the pitch during a game against AEK Athens earlier this month while appearing to carry a gun in a hip holster.
The Greek Super League disciplinary committee docked the club three points, ending their title chances, and fined them €63,000. PAOK have also been ordered to play their next three home games behind closed doors.
Meanwhile, AEK Athens were awarded the match, abandoned after the chaotic scenes in the closing moments, with a 3-0 scoreline.
The incident happened when, with the score at 0-0, PAOK had an 89th-minute goal ruled out for offside. Savvidis, a businessman who was born in Georgia and is a former Russian state Duma deputy, marched onto the pitch, accompanied by bodyguards, in protest.
He had to be restrained as he vented his fury, with images seeming to show there was a firearm attached to a holster on his hip. Savvidis made no visible move to use the weapon, for which he has a license.
The game was abandoned and the league suspended by the country's government, while a prosecutor ordered a judicial investigation to be carried out.
FIFA said on Thursday a panel it appointed last year to oversee the troubled national federation has filed a report about the Greek league being cleared to resume.
"Beyond the lifting of the ban, FIFA requires concrete guarantees that episodes of violence will stop thus allowing for a smooth running of the national competitions, both in the short and long term,'' FIFA said in a statement.
In a statement published on PAOK's website in the aftermath of the incident, Savvidis said: "I wish to apologise to all PAOK supporters, Greek fans and the international football community. I am deeply sorry for what happened. I had absolutely no right to enter the pitch the way I did.
"My emotional reaction stems from the widespread negative situations prevailing in Greek football lately and from all the unacceptable, non sports-related events that took place towards the end of the PAOK-AEK Athens encounter.
"The actions of the referee and his assistant, the match suspension, the protests and invasion on the pitch by many people from both sides, all that could lead to uncontrollable situations.
"My only aim was to protect tens of thousands of PAOK fans from provocation, riots and human casualties. Please believe that I had no intention to engage in a brawl with our opponents or the referees. And, obviously did not threaten anybody."
Information from The Associated Press was used in this report.