Scott had an 8-under 208 total on the Huntingdale course. He Scott bogeyed two of the last three holes, missing 5-foot putts.
'It's just my putting that's bothering me,'' Scott said. 'I'm playing great. I really feel like I'm hitting the ball well and I've worked out a good way to get around this golf course.''
Fellow Australian Gavin Coles was second after a 69, countryman Robert Allenby (65) was two strokes back and Nick O'Hern (65), Craig Parry (66) and Steve Collins (75) followed at 211.
Aaron Baddeley shot a course-record 64 for a 2-under 214 total.
'Conditions were nice out there,'' Baddeley said. 'I spoke to Lead (coach David Leadbetter) this morning on the way out here and he'd picked up a really small thing in my swing from watching TV.
'I worked on that at the range for a few minutes and hit it good. That made all the difference.''
Nick Faldo of England had a 68 for a 215 total, leaving him seven strokes back. Americans Ty Tryon and Tom Watson were 11 shots behind, Tryon after a 74 and Watson after a 70.
Full-field scores from the MasterCard Masters