PAOK will also play seven home games behind closed doors and pay a fine of €282,500.
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Vladan Ivic was taken to hospital for treatment after the incident, which followed a 54th-minute brawl involving several players.
PAOK won the Greek Cup by defeating AEK Athens 2-1 in a final marred by violent clashes between fans that injured more than 40 people, two seriously.
After a scrappy start, United scored the goal that put the tie beyond any doubt after 16 minutes.
Zlatan Ibrahimovic's hat trick gave Manchester United a 3-0 win against St Etienne in a Europa League round of 32 first-leg clash at Old Trafford.
Manchester United will take on St Etienne in the Europa League's round of 32, while Spurs will face Gent and Villarreal have been drawn against Roma.
Manchester United's troubles away from home in Europe continued in a 2-1 defeat at Fenerbahce in the Europa League as Paul Pogba limped off injured.
Manchester United laboured to a 1-0 Europa League victory over Zorya Luhansk at Old Trafford as Zlatan Ibrahimovic headed home in the second half.
Shakhtar Donetsk, Olympiakos and Fenerbahce all crashed out of the UEFA Champions League in the third qualifying round on Wednesday.
Ajax: Davy Klaassen brace helps club reach Champions League playoff round with 3-2 aggregate win over PAOK
Shakhtar Donetsk began their Champions League campaign with a 2-0 win over Young Boys in the third qualifying round on Tuesday.
PAOK held Panathinaikos to a 1-1 draw on Tuesday to win the Greek league playoffs and earn a place in the qualifying round of the Champions League.
The Greek side confirmed on Wednesday that the 37-year-old has been dismissed due to "unsuccessful results."
Greece's government has canceled the Greek Cup a day after a semifinal was stopped because of fan violence.
Dimitar Berbatov turned to the only reporter he trusts given rumours about his future: himself.
Borussia Dortmund face a difficult draw for the Europa League round of 32 and could face the likes of Manchester United after losing 1-0 to PAOK.
Borussia Dortmund have strongly condemned the crowd violence that caused a stoppage in their Europa League match against PAOK.
PAOK, who currently sit 12th in the Greek Super League, confirmed in a statement that Berbatov has signed a one-year deal.
A statement on Thursday from the governing body says matches in the first, second and amateur third division remain suspended indefinitely.