McEwan (28) trailed by four shots going into the final round but a one-over-par 72 in the final round was sufficient to force the playoff while other contenders drifted out of contention.
Millbrook greenkeeper Prince finished in second place while the defending champion, Liam Balneaves, who set a course record of 62 last year's strokeplay, came in third.
This trio was followed by Matt Whittington (Invercargill) in fourth place, Michael Smith (Otago) fifth, Jamie Mead (Rangiora) sixth and Balmacewen junior Thomas Facer seventh.
Toby Crosbie (Lumsden) won the senior B title by an impressive eight shots from Murray Edgar (Otago) while Watene Hema (Ben Ohau) took intermediate honours by a nine-shot margin.
Sean Geary (Chisholm Park) was easily the best player in the masters (over-40) field, winning by eight shots from John Cunningham, of Oamaru.
The championship was the first Otago trial and the first outing in the new order of merit series.
Facer took an early lead with a sub-par 70, playing his second nine four under, with the assistance of an eagle 2 on the difficult sixth hole.
But a four over 75 on Saturday afternoon put Facer in a tie for second at the halfway stage.
Mead and McEwan shared the halfway lead while the big mover in the second round was Michael Minty (St Clair), who grabbed a share of the lead with 69, the best score of the day.
The leader board was shuffled again on Sunday morning, with Prince carding 68 to share the third-round lead with Mead.
Prince made three birdies and an eagle 2 on the 17th hole to set up a good contest in the final round.
McEwan lost a ball after driving on the third hole but drove the green with his second drive, to make a birdie 3 and minimise the effect of the two-shot penalty.
He birdied the fifth to get back to square and stayed within one or two shots of par on his way to the title.
The best round of the tournament came in windy conditions in the final round with Russell Newman (Taieri) making seven birdies to finish with 66.
