Scott, whose second shot at 18 on Sunday landed in the water, holed a 10- footer for bogey at the 72nd hole to win by a single stroke over Padraig Harrington. The young Australian climbed six places from last week.
Tiger Woods, who tied for 16th at Sawgrass, remained in first place for the 242nd consecutive week. Vijay Singh, Ernie Els, Davis Love III and Mike Weir rounded out the top five once again.
Jim Furyk, who had wrist surgery that could sideline him for up to six months, held on to sixth, followed by Retief Goosen. Harrington moved up five with his runner-up finish, while Stuart Appleby and Phil Mickelson each dropped a spot to complete the top-10.
Kenny Perry, who shared third place at the Players Championship, moved up one to 11th, followed by Scott. Chad Campbell fell three to 13th this week while David Toms also dipped three rungs to 14th.
Darren Clarke slipped one place to No. 15.
Scott Verplank, Jonathan Kaye and Fredrik Jacobson all dropped one spot to come in Nos. 16-18. Shigeki Maruyama and Robert Allenby once again rounded out the top-20.
Any player in the top-50 after this week's rankings who were not qualified for the Masters already, will receive invitations to Augusta National in two weeks.
Craig Parry, Todd Hamilton, Trevor Immelman and Brian Davis are now in the field at the Masters.
John Daly, despite an 80 on Sunday at the Players Championship, qualified for the Masters because he is currently in the top-10 on the money list, another way to gain admittance into the field.