"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 be only the second player after compatriot Robert Allenby in 2005 to win Australia's triple crown by claiming the Australian Open, Masters and 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 par 62 in his opening round.
He came into the final day at 16-under par, with rounds of 62, 70 and 68, four shots ahead of McIlroy who was a further four shots ahead of the next challenger.
That effectively made Sunday's final round a shootout between the No. 2-ranked Scott and Northern Ireland's McIlroy, who was the world's top-ranked player last year.
Scott was left to rue a series of missed birdie opportunities, failing to hole six putts from within 12 feet during his final round.
"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."
Both players took irons from the tee on the last hole and landed their shots adjacent to each other on the fairway.
Scott's approach landed ahead of the hole but a cruel bounce sent the ball flying through the back of the green.
Rather than pitch and run back onto the green, Scott chose to give his chip some loft. It failed to pull up, rolling onto the lower tier of the green and the local favorite did well to salvage a bogey.
McIlroy stood assessing his ten foot putt during Scott's excursions, and after Scott holed out, McIlroy rolled in a slow putt that just made it to the hole.
"I didn't think it was going to unfold the way it did," McIlroy said. "It's hard not to feel some guilt in the way I won it.
"Having a one-shot lead going into the last having it taken away from you right at the very end, it's tough."
McIlroy finished with an 18-under par tally of 270, a shot ahead of Scott who was a further six shots ahead of Australian John Senden at 11 under.
Senden and compariots Bryden MacPherson and Rhein Gibson, who tied for fourth at 9-under, all qualified for next year's British Open.