"I wouldn't say anything's amazing but everything's been pretty good this week," Fowler said of his game after posting a 20-under 193 total.
Matt Kuchar, a recent winner in Hawaii, carded 65 to jump into second place on 16-under, while Thomas (68) was another shot back.
Fowler's lead matched the largest of his PGA Tour career, but he will not be planning a victory speech just yet in view of his recent history at the Phoenix Open.
He held the 54-hole lead last year before finishing equal 11th, and three years ago lost a playoff after hitting a ball into the water at the 71st hole.
It was not the first time he did not convert. He is 1-for-6 when holding at least a share of the lead going into the final round.
Fowler has won only four times on the PGA Tour, and 13 runner-up finishes has raised questions about his ability to close out the victory.
Not that the massive Saturday gallery -- the most boisterous on tour -- cared as they cheered every good shot, and some of the bad ones too.
"It's nice to finally feel the game click a bit," Fowler said.
"Last week I was still working on swing stuff and it wasn't quite there and I wasn't able to make many putts either.
"One of the big things is continuing to drive it well all week and set up the rest from there.
"Haven't had to scramble a whole lot but when I've needed to I've got the ball up-and-down."
Kuchar, a model of recent consistency with two wins in the past three months, stayed within striking distance of Fowler with a six-birdie round.
Thomas started slowly before collecting four back nine birdies.
Fowler, who is sharing a house with good friend Thomas this week, did not shirk the issue when asked for his thoughts about Sunday.
"Stick with the same game plan tomorrow, see if we can wear out some fairways and have some fun," he said.
"We'll all be trying to beat each other's brains in. The guys you want to beat the worst are your buddies.
"I've led for three rounds now, why not four?"
(Reporting by Andrew Both in Cary, North Carolina; Editing by Greg Stutchbury)
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