Scott won 14 times worldwide since turning pro in 2000 before breaking through in his native land. He finished at 15-under 273 at New South Wales Golf Club.
The win followed Scott's worst season on the PGA Tour, where he made only nine cuts in 19 tournaments and had just one top-10 finish.
"I always thought I'd get my chance," Scott said. "It's so bizarre, this game, that off the back of such a bad year I finally played good enough to win down here.
"I've worked really hard even though I've played terrible all year. But it pays off. You've got to stick with it."
Five-time Australian Open winner Greg Norman presented Scott with the Stonehaven Cup. Norman missed the tournament because of shoulder surgery.
"This is very, very special to me to win here," Scott said. "This is going to be very sweet and something I will treasure for the rest of my career."
Appleby closed with a 75.
John Daly closed with a 71 to finish at 2 over. He will play next week in the Australian PGA at Coolum in Queensland state.