Despite trailing by four shots going into the final round at Royal Sydney, the Northern Irishman sunk a 15-foot birdie to card a round of 66 and clinch the title from the 33-year-old - who had led the tournament since shooting a course-record 62 in the opening round - after the Aussie scored a bogey on the last.
Scott was vying for a Triple Crown having won Australian Masters and Australia PGA titles last month and McIlroy expressed his sorrow to deny the 33-year-old.
Speaking to reporters, the 24-year-old, who had not won a title since the DP World Tour Championship in Dubai last November, said that he is relieved that he will end 2013 on a positive note.
"I wanted to get a win by the end of the season and I've been able to get one, but more satisfying than that is that I've been able to take on one of the best players in the world down the stretch and come out on top.
"Adam's a phenomenal player, a great competitor and probably an even better guy. I feel a bit sorry that I was the one that sort of ruined the Triple Crown for him, but I'm very happy and Adam should be very proud.
"He's a credit to the game and he's also a credit to this country."
Robert Allenby remains the only player to win all three Australian titles in the same year, having achieved the feat in 2005.