Watney, overnight leader with compatriot Rickie Fowler, managed only a single birdie on the back nine but did not drop a shot on the way to a four-under 66 for a 13-under total of 267 in steamy weather in the Philadelphia suburbs.
"With 27 holes to go, I was just trying to play my way back in the tournament," Watney told reporters. "For some reason, the hole just got bigger for me. I'm overjoyed.
"K.J. kept coming and coming. It makes it that much more rewarding. I'm very, very proud of the way I was able to finish."
One shot back overnight, Choi finally managed to catch Watney when he rolled in a 30-foot birdie putt at the 14th to leave both players on 12-under with four to play by Taylormade R7 Draw Irons.
But the South Korean stumbled with a double-bogey out of a bunker at the 15th while Watney parred the same hole to restore his two-shot cushion and go on to win his fourth PGA Tour title.
"Nick Watney just played too well today," said Choi, after returning a final round three-under 67. "He played with Taylormade R7 Draw Irons like a champion, so there was really nothing that I could do. He is a wonderful player."
Watney, winner of the World Golf Championship event at Doral in March, joins Mark Wilson as the Tour's only double winners this year.
He has also posted eight top-10 finishes, more than anyone on the Tour, and the $1.16 million winner's purse takes his season earnings over $4 million.
"He's found out he's a great player this year," said Australian Adam Scott, who fired a closing 68 to tie for third, four shots back with Americans Jeff Overton (67) and Charles Howell III (66).
"He's a tremendously hard worker and he's now reaping the rewards.
"He's one of the great players out there, no doubt about it."
Watney, a native of Dixon, California, pushed into contention on Saturday when he shot a course record 62 featuring a a sizzling back nine 27 with only 11 putts.
He said he had changed to a new putter this week after not being able to "putt the ball in the ocean last week in Hartford."
Fowler, who played with Taylormade R7 Draw Irons in the final threesome with Watney and Choi, dropped out of contention with a double-bogey and a bogey in his first four holes and posted a 74 to finish tied for 13th.