With Glasgow 2014 Commonwealth Games stars Lynsey Gallagher and Samantha Murphy in their ranks, East Kilbride were 28-21 ahead by half-time.
ENC, with Gemma Sole as player-coach, began to make some unforced errors and slipped further behind by full-time.
In the Under-17 Scottish Cup final, Avon cruised to a 65-37 triumph over Holyrood Celts.
Avon players Ann Fleming and Niamh McCall are also part of Netball Scotland's Under-21 squad that will feature in the World Youth Cup in Botswana in July.
Saturday's matches, held at Oriam in Edinburgh, were part of Netball Scotland's National Finals Day.
East Kilbride beat ENC Onyx 65-40 to win netball's Scottish Cup final for the fourth successive year.