One PAOK supporter was also reportedly stabbed on Friday as fans of the Thessaloniki outfit, AEK and Olympiakos fought in the capital the night before the game, which PAOK won 2-0.
The Greek government deployed 5,000 police officers to try and prevent violence.
But two riot-trained police officers were left hospitalised, according to local media reports.
A Molotov Cocktail thrown by AEK hooligans set ablaze a van with five PAOK supporters inside near the stadium.
Media reports said two of the passengers were injured after being beaten up and were taken to a local hospital.
Each team were issued only 17,196 tickets at the 69,618-capacity stadium with many gaps to keep supporters separated for safety reasons, after a season of high tension between PAOK and the Athens clubs.
For the first time in 43 years a foreign referee was used in the Greek Cup final, with 44-year-old Spaniard David Borbalan being called to duty.
Earlier this year, PAOK president Ivan Savvidis stormed onto the pitch with a holstered gun on his belt during a match against AEK, after becoming incensed over a refereeing decision.
AEK later pipped PAOK to the Super League title after the latter's appeal against a three-point deduction failed.
Crowd violence has been prevalent all season, with former Olympiakos coach Oscar Garcia being injured in February when he was struck in the face by a cashier's roll thrown by a PAOK fan.
On Saturday, AEK missed out on a first double since 1978 as goals from Vieirinha and Dimitris Pelkas gained PAOK a measure of revenge for their defeat in the league title race.
It was their second straight Cup final triumph over AEK, after a 2-1 win last season which was also tainted by violent incidents before the match.