Scott closed with a 4-under 66 to finish his fourth tour win at 11-under-par 269. He was the lone player this week to post four rounds in the 60s.
'It's been a long time coming for me,' said Scott, who collected $1,170,000 for the win. 'It's been a while since I've won a four-round TOUR event. I seem to be the king of the rain shortened ones right now.'
Jim Furyk put some pressure on Scott, but came up three strokes short. He closed with a bogey-free, 5-under 65 to take second place at minus-8. Second-round leader Joe Durant was one stroke further back after a final-round, 3-under 67.
Two-time U.S. Open winner Retief Goosen ended alone in fourth at 6-under-par 274 after Sunday's 67. Luke Donald, Trevor Immelman and Tom Pernice, Jr. shared fifth at minus-3.
Vijay Singh, who played in the final group with Scott, struggled to a 2-over 72. He was joined in eighth place at 2-under-par 278 by Lucas Glover (68).
Scott led by three entering the round, but Singh cut the deficit to two with a birdie on the first. That would be as close as anyone got on this day.
The 26-year-old Scott ran in a 17-foot birdie putt on the third at East Lake Golf Club to regain his three-stroke cushion. He parred the next three holes, but remained three ahead.
Scott sank a 12-footer for birdie on seven to maintain the three-shot cushion as Furyk and Durant, playing one group ahead of Scott, also birdied the seventh.
The Australian dropped his approach 14 feet from the hole at nine and poured in that birdie putt. Scott came right back with a 9-footer for birdie on 10 to push his lead to four over Furyk.
Scott holed a bunker shot from short of the 13th green to extend his lead to five. He started to cruise from there. Scott's birdie putt on 14 lipped out, then he two-putted for par at 15.
He knocked his second shot over the green on 16 and faltered to a bogey there. Scott drained a 20-footer for par on 17 to take a comfortable three-shot lead to the last.
Scott's 30-footer for birdie on the last stopped just short of the cup. He tapped in for his fourth TOUR title. If that birdie putt had fallen, Scott would have become the first player since Shigeki Maruyama to birdie No. 18 in the final round since 2002.
'I played really good this week,' Scott stated. 'Just a couple of hiccups coming in, but managed to make a couple putts today and I really proud of what I did. I played great this week.'
Furyk made his run on the front nine, but he couldn't get over the hump on the back nine. The 2003 U.S. Open champion got on the board with a birdie at the first. He birdied the sixth and came right back with a 10-footer for birdie on seven.
The 36-year-old converted an 18-footer for birdie on nine to get within two of Scott's lead. Furyk only managed one birdie, on No. 14, around the turn. He two-putted for five pars and got up and down for the other three pars on the closing nine.
Stuart Appleby (70) and Ernie Els (72) tied for 10th at 1-over-par 281.