Playing more than his share of holes from sand, fringe, rough or first cut, Scott mixed seven birdies with three bogeys. His total of 18-under 195 tied the 54-hole course record set by Hal Sutton in 1991.
Scott also tied the lowest 54-hole total on the PGA Tour this year. Phil Mickelson carded 195 through three rounds at the Bob Hope Classic, and David Toms did the same at the St. Jude Classic.
Scott missed only two greens in regulation in setting the course's 36-hole record in perfect weather Thursday and Friday. But he missed three greens in his first nine holes Saturday as he battled swirling winds that had flags flapping. His bogey at No. 9 allowed Rich Beem to move into a tie for the lead, then Scott moved back ahead for the rest of the day with a 12-foot birdie putt at No. 10.
He then birdied the 13th and 14th, the two easiest holes on the course, before he found the rough again with his tee shot at the 15th and made bogey.
Scott then threatened to turn the tournament into a rout with a birdie at No. 18 as the rest of the field struggled with the winds and bumpier greens.
Olin Browne (71) bogeyed two of his last three holes, but was second with a 201. Charles Howell III (72) and Arron Oberholser (68) were seven shots back at 202.
Glen Day, who shot a 62 and threatened the 50s on Friday, threatened the 80s on Saturday with a 79.
Scott is No. 15 in the world, the highest-ranked player at this tournament. He has played in this Presidents Cup and won the Players Championship in March, but the 23-year-old Australian isn't yet a big draw in his first appearance at Avenel.
'What's Scott's first name?' a curious fan in the gallery said out loud after watching Scott birdie No. 8 with a tidy wedge to 2 feet.
Scott might have wanted to remain anonymous after landing in bunkers on three of four holes on the front nine, although he managed to save par on two of them. His early highlight was a nice chip from 76 feet that landed a foot from the pin at the par-5 sixth, setting up a birdie.
Beem, the 1999 champion, faded badly on the back nine, where he bogeyed Nos. 12, 13, 14 and 15. The 14th is a short par 4, but Beem put his tee shot in the creek.
He dropped his putter in frustration after missing a 10-foot par putt at the 15th. He shot a 72 for a 203 total, eight shots off the lead.