After trailing for most of the homeward nine, McEwan sank a 4m downhill putt on the first green for a birdie 4 and the title.
The event had been won by Vaughan McCall (Gore) in 2008, Harper in 2009 and Liam Balneaves (Greenacres) last year but McEwan played some superb golf to break the Southland run.
Tyrone Ratahi (Otago) recovered from his first-round loss to win the senior plate while Kayne Wardell (Otago) took senior B honours.
Wanaka's Simon Hollyer finished strongly after a lacklustre start to win the senior B plate, 14-year-old Cody McMullan (Chisholm Park) became the intermediate champion, and Paul Hubbard (Otago) took the junior title.
McEwan (30) last won the feature title in 1999 and yesterday's win was timely for the Otago No 1 as it forced him to show his best form this season.
Both finalists shot 66 with a barrage of birdies in one of the best finals in recent years.
Harper looked in control as the match came to an end but McEwan stuck to him like glue, awaiting his chance to strike back, which came only on the final hole.
Harper took first blood with an easy eagle 3 on the first after hitting to within 2m of the cup with his three wood second shot.
McEwan chipped in for a birdie 3 at the second to square the match and went one ahead with a birdie 3 at the short third hole.
Harper dropped a 3m putt for a birdie on the fourth to get back to square while a par 4 was good enough for McEwan to again lead when Harper struck an almost impossible lie on the par 4 fifth.
The pair halved the sixth in birdies while Harper made a birdie 2 to even the match at the seventh.
Three putts cost McEwan the ninth but it was Harper's turn to make a bogey at the 10th and the game was again square.
Harper sank an 8m putt for a birdie 3 at the Glen to get his nose in front, a lead he held until the final hole despite the pair halving the 13th, 16th and 17th holes in birdies.
Harper looked set to take the title when both players finished short of the 18th green but he chipped well past the hole, giving McEwan a chance to win the playoff.
In the morning semifinal matches, Harper took an early lead over Scott Hellier (Gore) and was never threatened while McEwan, following on from two large wins on Sunday, was five up on Hobbs with five holes to play.
But he bogeyed 14 and 15 while Hobbs made a birdie 3 at 16 and McEwan only took the honours with one hole to spare when the pair halved the 17th.
Otago team
For SI Interprovincial
Otago team to compete in the South Island interprovincial team tournament on the Otatara course in Invercargill on November 5-6.-Brent McEwan (St Clair), Andrew Hobbs (St Clair), Tyrone Ratahi (Otago), Chris Snow (St Clair), Mitch Bosley (Wanaka), Michael Smith (Otago), Simon Hollyer (Wanaka), Luke Murdoch (Otago).
Travelling reserve: Thomas Facer (Otago). Manager: Bill Trewern
