Morikawa also posted a 62, his featuring nine birdies and an eagle.
With the winds that so often buffet the Plantation Course again largely absent, five players posted rounds of 10-under or better.
Matsuyama's gave him a 54-hole score of 192 -- one stroke better than the previous 54-hole tournament record.
Japan's Matsuyama, the 2021 Masters champion, got things going with a run of four straight birdies from the third through the sixth. He rolled in a 58-foot birdie putt at the par-five ninth to make the turn level with Morikawa.
After birdies at the 10th and 12th he took the lead for good with a three-foot birdie at the 14th. That launched a run of three straight birdies, and Matsuyama kept the momentum with an unlikely par at 17 after his tee shot wound up on the wrong side of the cart path.
He closed with a birdie at the par-five 18th, where he muscled his second shot to the edge of the green and two-putted to maintain his advantage on Morikawa.
"Collin played well and I just kind of followed him, so good day," said Matsuyama, who is closing in on his 20th professional win and his 11th on the PGA Tour.
Morikawa hit 12 of 15 fairways and every green in regulation. He kept the pressure on Matsuyama all the way, starting with an eight-foot birdie at the fist.
After birdies at the third and fourth he curled in a 26-foot eagle putt at the fifth and was six-under for the day after a birdie at the ninth.
He added birdies at 11 and 12, and another pair at 15 and 16 before closing with a birdie at 18.
"Today was really, really good," said Morikawa, whose six PGA Tour titles include the 2020 PGA Championship and the 2021 British Open. "Couple shots out there (were) a little squirrely, but for the most part the irons were center face -- knew where they were going."
His most recent win was the 2023 Zozo Championship in Japan, where he ended a near two-year title drought, and Morikawa was delighted that work he'd put in during the off-season was paying off in the opening tournament of the season.
"It's nice to have it click together," he said. "It doesn't mean you're immediately going to finish top 10, top five, have a chance to win. But it's nice to be able to put it all together and shoot some scores in a tournament setting."
Sunday promised to be another Matsuyama-Morikawa duel. Belgian Thomas Detry was four shots behind Morikawa after a 65 for 197.
South Korean Im Sungjae carded an impressive 62 to claim solo fourth on 198 while England's Harry Hall posted a 66 for 199.
World number one Scottie Scheffler wasn't among the 60-strong field after hurting his hand in a Christmas Day cooking accident.
