Referee Demetris Mashias halted play at the Tsirion Stadium late into the first half after the boy was struck by a firecracker hurled by visiting fans.
The boy, believed to be a AEL Under-15 youth player, was rushed to hospital by ambulance but his condition was not immediatley known.
The injury was followed by a rain of fire crackers and missiles hurled by Apoel supporters onto the pitch forcing match official Mashias to interrupt the game and head for the dressing rooms.
The match resumed a half hour later until Mashias again whistled a stop when fans began showering the pitch with flares. Some opposing fans then made it to the edge of the pitch and began hurling objects at each other. Police in full riot gear moved in to keep them apart.
The match resumed for a second time, more than an hour later, with most fans having already left. The game finished locked at 0-0.