Calcavecchia finished the tournament at 5-under-par 275, which was the highest winning score on the PGA Tour this season other than the U.S. Open and PGA Championship.
Ben Crane, who won this year's U.S. Bank Championship in Milwaukee, fired a 4-under 66 on Sunday to get within one of Calcavecchia. Ryan Moore, who captured last year's NCAA Individual Championship and the U.S. Amateur title, birdied the 72nd hole to shoot an even-par 70 and join Crane in second at minus-4.
Jesper Parnevik narrowly missed a birdie try on the 18th Sunday, but carded a 2-over 72 and took fourth place at 3-under-par 277.
Calcavecchia began the final round with a one-shot lead, but with how difficult Shaughnessy Golf & Country Club played all week, pars were good scores.
He opened with four straight pars before a birdie at No. 5. He dropped a shot at the 10th as well, but still held the lead as Crane drained a 9-footer for birdie at 17 and a 15-foot par save at the last to get within two at minus-4.
Calcavecchia drove into the rough at the 13th and was forced to pitch out into the fairway. He knocked his third 10 feet right of the hole, but missed the putt to shrink his lead to one.
Once his lead was almost gone, Calcavecchia certainly gave himself some good birdie chances.
The 45-year-old drove into a greenside bunker at the short, par-4 14th and blasted out 5 feet past the stick. He missed that putt, then lipped out a 12-footer for birdie at the par-5 15th.
Calcavecchia hit his approach 40 feet long at the 16th, but his flat stick turned around as he lagged the putt to tap-in range. His 25-footer for birdie at the par-3 17th burned the left edge, but did not fall.
Moore hit a spectacular approach at the 18th that stopped 3 feet from the hole. He kicked in the short birdie putt to match Crane at 4 under as Calcavecchia had to play the difficult closing hole.
Calcavecchia hit a great drive down the fairway that left him with a 6-iron. His second rolled up to 4 feet, and Calcavecchia had two putts for the win. His first lagged close and Calcavecchia tapped in for par and the victory.
'I was so nervous out there in the fairway,' admitted Calcavecchia, who pocketed $900,000 for the win. 'I hit a great drive and the wind calmed down just perfectly. I really didn't want to hit a 5-iron and I hit a great shot.
'I didn't even think about making that one. I haven't made any all weekend, why make that one? Thank God I could two-putt.'
Joey Sindelar shot a 2-under 68 on Sunday and tied for fifth place with Jerry Kelly, who only managed a 1-over 71 in the final round. The duo came in at 2-under-par 278.
Vijay Singh, who won this title last year, struggled to a 2-over-par 72 and shared seventh place with Stephen Ames, who also shot a 72 on Sunday, and Trevor Immelman, who posted an even-par 70. The trio was knotted at 1-under- par 279.
Arjun Atwal carded a 2-under 68 and finished alone in 10th at even-par 280.