Scott would have moved up a spot to No. 3 in the world with a victory, and he opened with a three-stroke lead. He had a share of the lead with Austin through 12 holes before falling apart with a triple bogey and four bogeys down the stretch.
He finished with a 75 and finished seventh at 276.
"I'm going to be hard on myself. I really should be,'' Scott said.
Only Austin responded with his best finish since tying for seventh at the 2006 Buick Open. A self-taught player, he identified a flaw in his swing two weeks ago and had been working to turn his club to the inside on his downswing with his caddie, Brent Henley.
The changes clicked nearly perfectly Sunday with great iron play, including a lob wedge holed out for eagle from 64 yards out on the par-5 No. 5. Combined with a birdie on No. 2, Austin felt everything come together on the par-4 No. 7 when he hit right at the pin.
He parred that hole by two-putting, but his best shot came on the par-3 No. 14 - the toughest hole on the course with water guarding most of the green. He stuck a 5-iron within 3 feet for birdie, and what had been a one-stroke lead over Scott suddenly became a three-stroke lead.
Austin finished off what he called his best round other than the 57 shot once at home with birdies on Nos. 16 and 17. He celebrated the 16-footer on the par-4 17th with a fist pump, followed up by one more just for good measure.
"That was a true round of golf and was one of those surprises that we all get every once in a while,'' Austin said. "I'm just happy it happened to me on a Sunday when it really mattered.''
He became the fifth player in his 40s to win on tour this year, and his five-stroke victory matches the largest margin this year. Phil Mickelson, who withdrew from the event to allow a sore wrist to heal for the Open, also won by five at the AT&T Pebble Beach.
Divots: Austin's comeback was the best at this event since Len Mattiace won after trailing by seven in 2002. ... The previous low final round by the winner of this tournament was a 7-under 64 by Jay Haas in 1992, Mattiace in 2002 and Toms in 2003. Austin's 62 was the best final round since Nick Price shot a 62 in 2004 but finished tied for fourth. ... With 4,500 points, Austin moved from 145th in the FedExCup points race to 29th, or as he put it, "From outside to inside. I wasn't even inside.''