Castillo made it 3-0 in the 89th after dribbling past three defenders in the area.
The final was the last major game for AEK's Portuguese coach Fernando Santos, who announced on Monday that he would step down at the end of the season after two years. No reason was given for the departure.
AEK is in second place in the league and chasing a berth in the Champions League.
AEK fans trash ferry
AEK Athens supporters damaged a ferry carrying them home from Wednesday's Greek Cup final defeat to rival Olympiakos, throwing bottles and other objects.
Two people were injured, police said yesterday. One was a crew member hit by a bottle and the other a coast guard on shore hit by a flare fired by a fan on the vessel.
No arrests were made, police said.
Riot police waited yesterday morning for the ship's return from the island of Crete to the port at the eastern Athens suburb of Rafina.
"I was watching people throw objects into the sea. The crew tried to stop them but failed," ship captain Vassilis Paschalis said.
There more than 680 AEK supporters on the Ierapetra and Paschalis said 30 to 40 fans were involved in the damage to the ship's bar and salon.
Trouble started shortly after the ship left port at 10pm for the 12-hour journey. The boat was charted by AEK from Greek shipping company LANE.
Unconfirmed reports said fans caused an estimated 150,000 euros (US$190,000) damage.
As well as losing the final, AEK fans were reportedly upset by the price of their boat tickets and said they had been promised free food and drink.
More than 1,000 police had been on duty on Wednesday at the Pancrition Stadium in Iraklio, fearing possible clashes between supporters. Eight fans were arrested before the match for carrying fireworks.
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