The home victory gave APOEL an unassailable seven-point lead with only two games left to play, sparking celebrations in the capital.
They secured the title a week after parting company with their Georgian coach Temur Ketsbaia.
The Nicosia club will now represent Cyprus in the Champions League next season and will enter in the second qualifying round.
They made Cypriot history by becoming the first team from the island to reach the Champion League quarter-finals in 2012, when they were eliminated by Real Madrid.
APOEL, the island's most successful club, have now won a total of 25 Cypriot championships.