The Briton nervelessly sank a 10-foot birdie putt at the 18th to finish on 18-under-par for the tournament with a final round seven-under 66.
Scott, seeking a rare ‘triple crown’ of Australian titles after winning his country's PGA and Masters titles last month, led by a stroke going into the 72nd hole after McIlroy had eaten away his four-shot overnight lead in the first eight holes.
Two-times major champion McIlroy and Scott played together over the final two rounds in front of packed galleries at the Royal Sydney Golf Course but the Northern Irishman never led the US Masters champion until the final stroke of the tournament.
Image: Rory McIlroy
Photograph: Mark Metcalfe/Getty Images
ICC Test rankings: India retain second spot
Nadal-Djokovic French Open semis 'Best Slam Match of Year'
PHOTOS: Eight-year-old Messi lookalike a huge hit in Argentina
Dipika Pallikal gets engaged to Indian cricketer Dinesh Karthik
I don't need Ballon d'Or to know I'm the best: Ibrahimovic