Most of the arrests took place in Nicosia Wednesday night, when Omonia fans took to the streets of the capital to celebrate a 13th cup title for the island's best-supported club.
Five people were arrested outside the police station in Nicosia's downtown Lykavitos district when a crowd with fireworks and flares blocked a main intersection, hurled objects at police and set fire to rubbish bins, police spokesman Michalis Katsounotos said.
Another six were arrested on suspicion of stealing a car and possessing offensive weapons.
The main streets of downtown Nicosia were clogged with honking cars, trucks and even a front-end loader packed with cheering, flag-waving fans.
Katsounotos said that at around 11:00 pm, about 500 hooded hooligans -- some wearing Omonia shirts and scarves and carrying clubs and Molotov cocktails -- rampaged through the garden of a bar attacking customers.
Five people were hurt, but it was not clear if they were all patrons of the bar.
Another four people were arrested before the closely fought final staged in Larnaca, where the GSZ stadium suffered damage, and another fan immediately afterwards.
Details were not immediately available on the other arrests.
The game went to penalties, when both teams played out a 1-1 draw in regulation and extra time. Omonia won the cup 4-3 on penalties.
There had been huge pressure on Omonia to lift some silverware at the end of the season after fierce Nicosia rivals APOEL eased their way to the league title.
This is not the first time a big football occasion has been spoiled by hooliganism, which has become a common feature of Cyprus sporting events.