McIlroy, seeking his first victory since the European Tour's season-ending DP World Tour Championship in late November, parred the last three holes on the brutal closing stretch to post a 12-under total of 204.
"I just played a really solid round of golf," he told Golf Channel after getting up and down from a greenside bunker to save par at the last. "I didn't make any mistakes, no bogeys, which is what I've been looking to do.
"I feel like I've been making too many mistakes, so to eliminate the mistakes out there today and hole a lot of good putts and give myself a lot of (birdie) looks, I felt really good about it," added McIlroy, who is seeking his 12th PGA Tour win. "I just need to do more of the same tomorrow."
Australian Scott, winner of the Honda Classic last week, bogeyed two of the last six holes on the way to a 73 and a share of second at nine-under with long-hitting American Dustin Johnson (71).
Two ahead of the chasing pack overnight, Scott bogeyed the par-three fourth after missing the green off the tee to fall back into a tie for the lead with McIlroy, who picked up a shot at the opening hole.
McIlroy sank a seven-foot birdie putt at the fifth to edge a stroke in front before doubling his lead when he drained a 16-footer at the par-five 10th.
The Northern Irishman, using a deft short game, parred the last eight holes to maintain his grip on the tournament.
"It feels really good," McIlroy said of his change this week from a conventional putting grip to left-hand low, following a missed cut at the Honda Classic.
"I feel really comfortable over it and you can see by the way I have been putting, I have been holing a lot of the putts that I should hole to keep the round going.
"It's so nice to hole a putt like that on the last just to give myself that little bit of a cushion going into tomorrow," he said of his six-footer for par at 18.
World number one Jordan Spieth was tied for 17th at two-under after a 73.
(Reporting by Mark Lamport-Stokes in Los Angeles; Editing by Larry Fine)
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