Perry and Huston used a string of six straight birdies on the back nine to take the lead over a low-scoring field. They finished the three-day event at 30-under-par 186 to split a $630,000 paycheck.
Mark O'Meara and Nick Price combined to shoot a 12-under 60 and finished alone in third place at minus-27.
Tournament host Greg Norman and partner Steve Elkington stole the spotlight early on by tying the tournament's scramble record with a 17-under 55 to finish in fourth place at minus-26.
Norman and Price were the first team to shoot a 55 in the scramble round when they did it in 1993, and the mark was later matched by John Cook and Peter Jacobsen in 1998.
Couples and Scott thrived in the scramble format for the first 10 holes, collecting seven birdies during that stretch to reach 26 under. But Perry and Huston tied them with a birdie at the 12th.
Both teams then birdied the 13th to move one stroke clear of Norman and Elkington, who were already in the clubhouse.
At the 14th, Couples and Scott could only make par from a fairway bunker after both missed 10-foot birdie putts. Huston then tapped in from 2 feet for a birdie that gave him and Perry the lead for good at minus-28.
The duo extended their advantage to two strokes when Perry made an 18-foot putt at the 15th for their sixth straight birdie. That lead was trimmed to one shot when Scott rolled in a 60-footer for birdie at 16 to get to minus-28.
After both teams birdied the 17th, Couples was the only player to hit the fairway at the par-4 18th. Huston and Scott found a bunker, while Perry landed in the mulch left of the fairway.
But it turned out to be a missed opportunity for Couples and Scott, who couldn't get it closer than 20 feet on either of their approach shots. Both missed their birdie tries -- Couples to the right and Scott to the left -- before Huston tapped in from 2 feet for a par and the win.
For Huston, who replaced Scott Hoch as Perry's partner, the victory provided a brief respite from what has been a year full of struggles on the course.
'It's been a tough year,' said Huston, who ranked just 120th on the money list after 31 events. 'But maybe I was a little relaxed this week...and I had a horse, I mean he (Perry) just played great.'
The feeling was mutual.
Afterwards, Perry declared Huston 'king of the Bermuda grass.'
'He's just the best on Bermuda, and he taught me a lot in the past few days,' Perry said of his partner. 'We were very relaxed and very easy going...He played beautifully, and I just kind of hung on as he drove me around this place.'
First-round leaders Fred Funk and Jason Gore shot a 7-under 65 in the scramble and shared fifth place with John Daly and Tim Herron (60) at minus-23.
Ryan Moore and Jesper Parnevik (64) ended alone in seventh place at 22 under, while Paul Azinger and Olin Browne (61) shared eighth place one stroke further back with Mark Calcavecchia and Loren Roberts (62).
Hank Kuehne and Jeff Sluman, who came in as the two-time defending champions, finished with an 8-under 64. They shared 10th place at 19-under with Kirk Triplett and Jay Haas (65).
Jacobsen and Scott McCarron were last at minus-16 after a final-round 63.