Making his first appearance back in Australia since his April win at The Masters, Scott finished with a 14-under 270 at Royal Pines.
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Scott joins Greg Norman, Craig Parry, Peter Lonard, Robert Allenby and Peter Senior as the only Australian golfers to add the Joe Kirkwood Cup for winning the Australian PGA to the Australian Open and Australian Masters titles in their careers. Those three tournaments are considered the Australian majors.
Scott's shot on the 12th came on a 4-iron from 266 yards.
"I came out and knew I had to do something great to win this," Scott said. "It's been an incredible year since April, and so great to come home. I've had a great week."
Fowler said the storm suspension hurt him.
"I had some good momentum going up until we had the rain delay," Fowler said. "I got to within one and then he came out swinging.
"He made some great swings coming down that last stretch. So it's a little tough to catch a guy when he's making an eagle and a couple of birdies."
Scott moves on to Royal Melbourne next week to defend his Australian Masters title. Then he will play with Jason Day on the Australian team at the World Cup, also at Royal Melbourne, then will play at the Australian Open at Royal Sydney a week later.
