Thomas, who started the day two strokes behind halfway leader Scheffler, started applying pressure with four birdies on the front nine at Albany Golf Club in the Bahamas.
A 47-foot birdie putt at the 14th put him atop the leaderboard at 16-under and he made a three-foot birdie at the 16th to reach 17-under 199 through 54 holes in the unofficial event.
"I'm driving it great," Thomas said. "I've had a lot of confidence with it. I feel like I've been able to put myself in some pretty good spots going into the green.
"I'm still not taking advantage of some of them as much as I would like, but that's golf and we're always going to say that," added Thomas, who hasn't won on the US PGA Tour since he claimed his second PGA Championship title in 2022.
A victory on Sunday wouldn't count as a 16th US PGA Tour title, but it would be a welcome payoff for Thomas's recent work.
"I've been progressing nicely, been working on all the right things," he said. "(I) feel like I've been seeing signs of improvement, which is what you want and that's all I can do."
Scheffler, whose eight titles this year included a second Masters green jacket and Olympic gold, had four birdies and a bogey in his three-under par 69.
His 16-under par total of 200 put him one clear of South Korean Tom Kim, who flirted with a 59 on the way to a 10-under par 62 for 201.
"I think it was decent," Scheffler said. "I had a stretch at 13, 14, 15 where I felt like I lost a shot or two there, but outside of that I did a lot of really good things today."
With increased winds making things tougher, Scheffler called Kim's 10-under round "pretty serious golf".
Kim opened with four straight birdies and rolled in a 19-foot birdie at the seventh and a 23-footer at the ninth.
That was the start of a three-birdie burst, that included a 39-foot putt at the 10th.
A sub-60 round looked possible after Kim made three more birdies at the 14th, 15th and 16th -- rolling in a 22-foot putt from off the green at 16 to keep a sub-60 round in sight.
But he fell back with a double-bogey at the par-three 17th, where his tee shot found the greenside bunker and his second shot hit the slope and rolled back into the trap.
Kim produced one final flourish, however, holing out from a greenside bunker for birdie at 18.
"I felt like I did a lot of smart things," Kim said. "Obviously I chipped it really good. I putted really well, did a lot of good things to keep my momentum going."
