The 29-year-old Scott finished with a combined 11-under 133 in a 36-hole finale Sunday to beat Swede Fredrik Jacobson by a shot.
The 2008 Byron Nelson Classic winner overcame two early bogeys with an eagle on the par-four 17th for a third round 66 earlier in the day on the Oaks Course at TPC San Antonio.
"It was a long, hard day, but sometimes when you get hot it's good to play 36 (holes)," said Scott, who earned just under 1.1 million dollars for the win.
Scott, who posted his seventh career win, survived a closing bogey when Jacobson missed a 16-footer from the fringe on No. 18 that would've forced a playoff.
"I certainly felt with five holes to go I could do something," Jacobson said. "I had good feelings coming from the morning. I gave myself good looks on all five of them. Just didn't happen."
More than three inches of rain had washed out Friday's round, setting up Sunday's 36-hole marathon.
Ernie Els, Aaron Baddeley and Jimmy Walker tied for third at 12 under. Els followed a third-round 69 with a 68.
Australia's Baddeley also entered the day four back and shot 67 and 68. Walker had rounds of 70 and 69 and ended up with a career-best finish on the USPGA tour.
Tim Petrovic and tour rookie Garth Mulroy were 11 under.
American JB Holmes had the 54-hole lead at 12 under but stumbled in the fourth round.
His had a double bogey on the par-four first then bogeyed four of his next seven holes.
Holmes was four over in the final round and finished at eight under.