"I knew what it meant and just the way the tournament finished for him. Having a one-shot lead going into the last and having it taken away from you right at the very end, it's tough.
"I've been in that position before.''
McIlroy, the one-time world No.1 and two-time major champion, started the final round four shots adrift of Scott but overturned the deficit with a bogey-free six-under 66 to finish at 18-under.
The victory ended a 13-month winless run for the now world No.6.
"I knew I was going to have to do something pretty special to catch Scotty,'' he said.
"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.''
It was McIlroy's 10th triumph worldwide and the 24-year-old admitted it was special to win what was once considered golf's fifth major.
"Gary Player, Arnold Palmer, Jack Nicholas, (Tom) Watson, (Peter) Thomson ... it's a trophy packed with true champions of the game, greats of the game,'' he said.
Scott had numerous chances to slam the door shut on McIlroy but will forever rue five lip-outs and a costly three-putt on the par-5 16th when he could have skipped three strokes clear with two holes to play.
"Nothing was going my way on the greens today,'' Scott said.
"I could have put this thing away early on if the putter was behaving how it should have, how it did the rest of the week.''
Scott had been hoping to join Robert Allenby as only the second player to complete the Triple Crown in the same season after also winning the Australian Masters and Australia PGA titles last month.
He also won the Australian Open in 2009 but was shattered not to have captured a second national championship.
"I'm gutted. I felt I'd never have a better chance to win the Aussie Open,'' he said.
Former champion John Senden closed with a 66 like McIlroy to claim outright third - and automatic qualification for next year's British Open - at 11-under.
Rhein Gibson and Brydan Macpherson also clinched Open berths by carding 69s on Sunday to share fourth spot at nine-under.
Jason Day (70), Matt Jones (72) and Kiwi Mark Brown (69) tied for eighth a further shot back at eight-under.
West Australian Brady Watt (72) was the leading amateur in equal 14th at five-under after 15-year-old Ryan Ruffels closed with a 73 to finish joint 24th at three-under.
- AAP