Defending champion Schauffele heads into Sunday's final day with a shot at retaining his title after carding a 6-under-par 65 to finish the third round 9-under overall.
The American had a roller-coaster front nine in sunny conditions in Yokohama, starting with a bogey before holing two birdies and an eagle on the par-5 fourth.
Schauffele followed that up with a double bogey on the next hole before sinking another eagle on the par-5 sixth, and went on to card four more birdies and another bogey to finish the round.
"It was a weird day," said Schauffele, who won Olympic gold in Tokyo in 2021.
"It was a lot of good, honestly some really bad in there as well.
"But overall, if someone told me I was going to shoot 65, I'd probably take it."
Michael Brennan, Zach Bauchou and Jacob Bridgeman lead the field heading into the final day on 13-under par.
Bridgeman is looking for his third win on the tour this year.
The trio hold a one-stroke lead over a chasing pack that includes Australia's Adam Scott.
Japan's Hideki Matsuyama is eight shots off the lead after a mixed day when he shot a 2-under-par 69.
Matsuyama, the 2021 champion in Japan, started like a freight train, rattling in four birdies and an eagle on the first seven holes.
He ran into serious trouble on the back nine, though, carding five bogeys and only one more birdie to undo much of his good work.
"It was a mix of great golf and the worst golf," said 2021 Masters champion Matsuyama.
"But it wasn't that I played absolutely terribly on the back nine.
"It was little things, so I just need to make some small adjustments to make sure that doesn't happen again tomorrow."
Three-time major winner Jordan Spieth was six shots off the lead after shooting a 3-under-par 68 to finish 7-under overall.
Spieth is looking for his first win on the tour since April 2022.
Collin Morikawa, the 2023 champion in Japan, was on 4-under overall.