MacKenzie led by three strokes with five holes to go and was ahead by one before he bogeyed the par-5 17th. Estes could have taken the lead there, but missed a 20-foot birdie attempt and missed another on the 18th from about 16 feet. He shot an even-par 72 in the final round.
He won a Nationwide Tour event last year and entered the week ranked 179th on the money list with $197,158. His previous best showing was a tie for eighth last year at the Michelin Classic at Las Vegas.
Joe Ogilvie was third after tying the course record Sunday with a 10-under 62, including 11 birdies -- eight of them on the back nine for a tourney-record 28 at the 7,472-yard Montreux Golf and Country Club course.
MacKenzie started the day tied with Estes at 19 under. He had two birdies and a bogey on the front nine and was 20 under through 13 holes, three ahead of Estes.
Estes, who has four PGA wins in 18 years on tour, came back with a birdie on the 491-yard, par-4 14th when he hit to within 7 feet of the pin. He followed that with a 10-foot birdie putt on the 15th to get to 19 under, one behind MacKenzie.
Both parred the next two holes but MacKenzie drove the ball 307 yards left into the rough behind some towering ponderosa pines on the 636-yard, par-5 17th. His third shot went 10 yards over the green into the rough.
He had a decent lie because the gallery had trampled down the 6-inch long grass but hit it too hard. The ball rolled 33 feet down hill past the hole and he two-putted from there for a bogey.
Estes missed his birdie attempt from 20 feet but still managed to grab a share of the lead by making par.
On the 18th, Estes' second shot spun back to about 16 feet beyond the hole while MacKenzie's approach stopped pin high about 10 feet left of the hole.
After Estes missed his birdie attempt, MacKenzie made his, raising his hands above his head and looking to the sky before hugging his caddie and kissing his girlfriend.
Daniel Chopra shot a 69 to finish in fourth at 17-under 271. Nick Watney (67), Jose Conceres (66) and Jeff Brehaut (69) were next at 16 under.
He set a tournament record with three eagles in the same round on Thursday when he also set the tourney record for low opening round with a 9-under-par 63 -- his career best. He added another eagle the next day, posting consecutive 67s before Sunday's closing round of 1-under 71.
Estes got off to a bad start Sunday with a a double bogey on the first hole, allowing MacKenzie to take an early lead.
They both birdied the par-5 fourth and Estes pulled within two strokes when he hit his approach to within 4 feet on the par-4 sixth and made the birdie putt. He also birdied the sixth to improve to 19 under, two behind MacKenzie
Mackenzie fell back to 20 under when he laid up 100 yards out on the 636-yard par-5 ninth, but hit his approach into a front bunker. He was forced to hit out sideways some 70 feet from the hole but was able to get down in two from there for a bogey.
But Estes also bogeyed that hole when he hit left into the sage brush and had to drop with a penalty. He laid up after that, but hit in the bunker before he was able to get up-and-down from the back fringe to remain two behind at the turn.