Another six PAOK supporters were arrested during clashes with police before and after Wednesday's match, which PAOK won 1-0 to advance.
The game was repeatedly halted by brawls on the pitch, with three players sent off, while PAOK fans in the stands lit thousands of flares, and several were thrown on the pitch.
Police said Thursday a 34-year-old man covered the Olympiakos bench in several kilograms of anchovies just before the game. Olympiakos' home ground is in Athens' port of Piraeus, and its supporters are nicknamed "anchovies."
PAOK plays Panathinaikos in the April 26 final. The Greek Football Association on Thursday said the final would be held as planned at the Olympic Stadium in Athens, denying reports of a possible move to avoid more crowd trouble.
Yiannis Andrianos, a minister for sport, described Wednesday's match as a "disgrace to Greek football," noting that players involved in the brawls included members of Greece's national team.
Nine members of the current 22-man squad are from PAOK and Olympiakos. Coach Fernando Santos is preparing his final selection for the World Cup where Greece faces Colombia, Japan and Ivory Coast.