The 39-year-old Millar shot a three-under 68 for a seven-under total of 206, breaking clear of a congested leaderboard as challengers crumbled in the trying conditions at Melbourne's Huntingdale Golf Club.
Millar had a one-stroke lead over compatriot Andrew Evans in second, with John Senden, a two-time U.S. Tour event winner, among a group of four a stroke further back on five-under.
Former world number one Scott, overnight leader by a stroke with Peter Wilson, fell five off the pace after a seven-bogey round that boasted just one birdie, on the second hole.
He was only marginally better than his playing partner, Victorian professional Wilson, who endured a horror 80 with eight bogeys and a double-bogey on the par-three 12th.
Millar, a part-time coach who lost his local tour card last year, bounced back to win the New Zealand PGA title and has been in the form of his life since.
"It's been a great year ... I always thought this (tournament) would be my best chance," the soft-spoken Canberra man told reporters.
"I'll probably lay awake all night ... It comes down to my own game. It couldn't be any further way to Adam Scott's game. I just marvel at what he does."
World number 12 Scott, bidding for a third Masters title in four years, brought his driver troubles from the third round and endured a miserable day on and around the greens.
The back nine again proved painful, as he notched consecutive bogeys on the 10th and 11th holes before dropping further strokes on 17 and 18.
American George McNeill, a two-time U.S. Tour event winner, shot a 73 but remained in contention at three strokes off the pace on four-under.
U.S. Amateur champion Bryson DeChambeau (72) was two further behind on two-under.
(Editing by Peter Rutherford)
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