The long-hitting Thomas, a winner in two of his last three PGA Tour starts, also recorded seven birdies and three bogeys to post a 17-under total of 123 in the first full-field event of the year on the U.S. circuit.
Despite finding the left rough off the tee at the par-five 18th, the 23-year-old struck a superb second shot from 205 yards to nine feet and coolly sank the eagle putt to post a landmark total at the tournament's halfway mark.
"I played great," Thomas told Golf Channel. "I really hit a lot of quality shots today.
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"The three bogeys I made were just terrible... a lack of concentration or just not playing smart but obviously I had a great day out there. To finish with that eagle was huge."
Thomas' 36-hole aggregate eclipsed the previous low of 124 jointly held by Pat Perez (2009 Bob Hope Classic), David Toms (2011 Crowne Plaza Invitational) and Jason Day (2015 BMW Championship).
TOO AGGRESSIVE
"Just like yesterday, any time you can get your name in the record books, it's awesome," said Thomas. "It's really cool to get a record like that."
Fellow American Gary Woodland, also known for his prodigious length off the tee, was alone in second place after carding a second successive 64.
Olympic champion Justin Rose (64) was a further two strokes back at 10-under, tied for third with Americans Hudson Swafford (68) and Zach Johnson, who fired a best-of-the-day 61.
Thomas, who became only the seventh player to break 60 on the PGA Tour, birdied two of the first seven holes on Friday before he bogeyed the eighth after pulling his tee shot left into a treeline.
He then rebounded with a run of four birdies from the ninth to stretch his lead to five strokes before he ran up another bogey at the 13th, where he bunkered his approach.
After lipping out with a birdie attempt from five feet at the 14th, Thomas picked up another shot at the 15th but bogeyed the par-three 17th where he paid the price for being too aggressive off the tee.
"The bogeys on 13 and 17 were a bit of a bummer but I made enough birdies on the back nine to kind of counteract that," said Thomas, who clinched his third PGA Tour victory at the SBS Tournament of Champions, also in Hawaii, on Sunday.
His other two PGA Tour triumphs came in Malaysia, when he won the CIMB Classic in Nov. 2015 and defended the title last October.
(Reporting by Mark Lamport-Stokes in St. Augustine, Florida; Editing by Peter Rutherford/John O'Brien)
