Fans invaded the pitch, clashing with riot police, and a goalkeeper was hit by a flare in the 1-0 defeat by AEK Athens in a semi-final second leg match at Salonika's Toumba stadium on March 16.
The punishment from the Greek football federation's disciplinary committee, which included the largest fine it has handed out this season, means PAOK will face Kerkyra in their last match of the regular season on April 17 without fans.
They will then begin their campaign for Greece's second Champions League place via the Super League end-of-season play-offs.
Last month's incident was the fifth pitch invasion of a season marred by violence inside and outside Greek stadiums.
A players' strike was narrowly averted last month after their PSAP union failed to get the backing of all 16 top-flight clubs - a move prompted as a reaction to the increase in crowd violence.
Top clubs Olympiakos Pireaus and Panathinaikos were handed supporter bans after hundreds of fans invaded the pitch, fighting police and attacking players following champions Olympiakos's 2-1 win over their closest rivals on February 19.
Attacks by supporters on the Super League offices and the home of Olympiakos player Vasilis Torosidis followed.
Panathinaikos assigned bodyguards to several players as the fall-out continued from what has been dubbed the "derby of shame" by Greek media.
