Scott, the winner of this year's Players Championship, established a new 36-hole record for this event with his 128 total. He broke the 130 mark Fred Funk set in 1998.
Charles Howell III, who broke the course record Thursday with a 10-under 61, posted a 2-under 69 on Friday and is tied for second with Olin Browne, who carded a 5-under 66 in the second round. The duo is knotted at 12-under-par 130.
Glen Day also fired a 62 on Friday and is tied for fourth with 2002 PGA Champion Rich Beem. Beem, who won this event in 1999, shot a 67 to match Day at minus-11.
Scott started on the second nine Friday and parred his first two holes. He knocked a 7-iron to 10 feet to set up birdie at the 12th and tallied back-to-back birdies at 15 and 16. Scott ran home a 6-footer for birdie at No. 18 to make the turn at 4-under-par 31.
The 23-year-old Australian wasted little time in getting into red figures on his second nine. He sank a 20-footer for birdie at the first, but parred his next two holes.
At the fourth, Scott hit a 6-iron to 20 feet and rolled in the birdie putt. He made it back-to-back birdies at the fifth with a 10-footer, then recorded his third birdie in a row at the par-5 sixth when he missed the green with his second, but chipped to 7 feet.
Scott had the 36-hole tournament record if he parred in, but the 15th-ranked player in the world padded his new mark. He holed an 8-foot birdie putt at the eighth to match his lowest round on the PGA Tour.
'I played really good the last two days,' said Scott, who also fired a 62 in the final round of last year's Honda Classic. 'I've not really been in too much trouble so far and I made my share of putts, which was nice.'
After Scott's impressive victory at the TPC at Sawgrass, he was considered a front-runner for the Masters two weeks later. He missed the cut at Augusta and missed the weekend in three of four events since then, but Scott seems to have pinpointed the problem.
'I really struggled with putting last week at the U.S. Open,' said Scott, who missed the cut at Shinnecock Hills. 'The greens here this week, I've seen a couple go in and got a really good feel for it.'
Howell came back down to earth after Thursday's round of two eagles, eight birdies and two bogies. On Friday, Howell was 1-over at the turn, but tallied three birdies on his second nine for his 69.
'As easy as yesterday seemed, today seemed a bit of a grind,' said Howell, who has only two top-10s in the 2004 season. 'I got off to an okay start, and any time you shoot 10 under, there is still a weird feeling about the following day. At the same time, I've got a chance here going into the weekend, which is not something I have been able to say very often this year.'
Browne was flawless for the second day in a row. He collected five birdies and finds himself in position for his first victory on tour since the 1999 Colonial.
'The good thing is a lot of the stuff I have been doing helps me identify the things that I've done well in the past and I feel like I'm starting to do those things again,' said Browne, who has made only four cuts in 14 starts this year. 'Maybe that can carry over on the weekend.'
Tom Lehman shot a 67 on Friday and is alone in sixth at minus-9. Bill Haas, the son of Jay Haas who is competing as a professional for the first time, carded a 65 and is tied for seventh with Arron Oberholser (65) and defending champion Rory Sabbatini (67). That trio finished 36 holes at 8-under-par 134.
The 36-hole cut fell at 1-under-par 141 and among the players who will miss the weekend are: Hank Kuehne (143), Justin Leonard (144), Scott Hoch (145) and Funk (146).