McIlroy spoils Scott's bid for Australian triple crown
McIlroy started the last round four shots behind Scott, but drew even when he eagled the seventh and birdied the eighth.
Scott went a shot ahead with a birdie at the ninth. The pair then went shot for shot over the back nine before the dramatic finish.
Scott's approach shot went over the back of the green and his chip went well past the hole, with two putts bringing a bogey. McIlroy hit his approach to 10 feet and sank the putt to win by a shot.
"Adam is a phenomenal golfer, a great competitor and probably an even better guy and I feel a bit sorry that I was the one that ruined the triple crown for him."
Scott was attempting to become only the second player after compatriot Robert Allenby in 2005 to win his country's Triple Crown by taking the Australian Open, Australian Masters and Australian PGA titles in the same season.
He carried his form from the Masters and PGA tournaments into the Open, shattering the course record with a 10-under 62 in his opening round.
In another tournament* At Malelane, South Africa, Charl Schwartzel successfully defended his title at the Alfred Dunhill Championship, shooting a 4-under 68 for a four-shot victory and his first European Tour victory in a year.
Schwartzel finished with a 17-under total of 271 to secure his third Alfred Dunhill title. Richard Finch was second, while Simon Dyson, Ross Fisher and Romain Wattel tied for third.