The Australian, who had trailed by three after the opening round, eagled the par-five 17th to forge two ahead of overnight leader Justin Rose, then parred the last for a course record seven-under-par 64.
Scott covered the last six holes in a sizzling four-under to post an eight-under total of 134 at the Port Royal Golf Course in the elite 36-hole event which brings together the winners of the year's four majors.
"Obviously I'm thrilled to come out on top," Scott told reporters after setting up his win at the 17th with a brilliant six-iron from 190 yards that finished a few inches from the cup for a tap-in eagle.
"Fun, but a trying couple of days here really, especially today. It felt like a long round out there but I was happy with the score. Standing on the 11th tee, didn't look like a score like that was going to be possible.
"But I played very well and managed to slowly claw away at Justin. After he made bogey on 16, I managed to capitalise on that by hitting such a great shot into 17."
Scott had covered the front nine in three-under 33, then birdied the 13th and 15th before seizing the outright lead with his eagle three at the 17th.
US Open champion Rose, who had been four ahead after making four consecutive birdies from the fourth, faded with bogeys on two of the last 10 holes on the way to a 69 and second place at six under.
"I started with a two-shot lead and somebody had to shoot well to beat me," said Englishman Rose, who had been two ahead of American Jason Dufner overnight after opening with a 67.
"When you're in that position you want to close it out, but when somebody finishes it out like that, you have to tip your hat and say, you were beaten rather than losing."
PGA Championship winner Dufner was a further three strokes back after closing with a 70 while defending champion Padraig Harrington of Ireland (71) finished at three over.
Harrington, a three-times major winner, was a late replacement in the field after British Open champion Phil Mickelson chose not to play.
- Sports & Recreation
- Port Royal Golf Course
- Justin Rose