The world number two was made to wait for his victory by a passing storm that stopped play for nearly two hours but he returned to the course to complete a final round of four-under-par 67 for a tournament tally of 14-under 270.
His American playing partner Rickie Fowler finished second at Royal Pines after a fourth round 68 to finish on 10-under with local youngster Jack Wilson (68) a further two shots back in third.
Adding the PGA to his previous victories at his home Open and Masters tournaments, Scott joined Greg Norman, Craig Parry, Peter Lonard, Robert Allenby and Peter Senior as the only players to have won all three of Australia's marquee titles.
(Reporting by Nick Mulvenney, editing by Amlan Chakraborty)
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