Two-time major champion McIlroy looked down and out after a patchy front nine but the Northern Irishman rallied for a 70 to remain in the hunt for his first win of the year in front of bumper galleries at the Royal Sydney Golf Course.
Most of the crowd were backing Scott's bid to secure a "triple crown" of marquee Australian titles in a month and they were delighted when he birdied the last to double his overnight lead by reaching 16-under for the tournament.
McIlroy, who missed a shorter birdie putt at the 18th, will resume on Sunday on 12-under, four shots clear of Australians Max McCardle, Matt Jones and Richard Green in a share of third.
Scott started the day with a two-shot advantage over McIlroy and with the sun shining brightly, it looked being a day of low scoring when both players birdied the opening hole.
McIlroy found himself in a thicket with his drive at the second but rallied to save par brilliantly as Scott lipped out with a birdie putt.
The Northern Irishman's bogey at the fourth was not a disaster as Scott followed suit after finding a bunker but the Australian opened up a four-shot lead as the wind whipped up at the fifth.
McIlroy undercooked successive chips from the bottom of a greenside slope and then two-putted for a double bogey, while Scott missed a 10-foot birdie putt but sank his second attempt from a foot for par.
Former world number one McIlroy was now buried in the chasing pack and when Scott picked up shots at the three holes before the turn he moved to 15-under, five clear of Jones and Green in second.
Scott drove into the trees and then the sand to take a bogey at the 10th, however, and McIlroy capitalised with the first of three birdies in five holes, the last coming after he hit the pin with his tee shot at the short 14th.
Scott was only a little less accurate with his iron for a birdie at the same hole and the marquee pairing were now clear at the top of the leaderboard with three strokes separating them.
Both found the greenside bunkers at the 16th but saved par, McIlroy just missing out on a birdie with a long snaking putt, and the pair got up-and-down from off the green for pars at the next before Scott drained his crucial five-footer at the last.
(Editing by John O'Brien)
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