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Walker, shocked by Patrick Reed in a playoff on Monday in the Tournament of Champions at Kapalua, showed he has put that disappointment behind him.
He one-putted his last 11 holes in round three and his 16-under par total of 194 gave him a two-stroke cushion over fellow American Matt Kuchar.
Kuchar, one of a trio who shared the overnight lead, carded a two-under 68 for 196.
Brian Harman and Troy Merritt shared third on 197, Harman signing for a 64 and Merritt posting a 67.
It was a further stroke back to South Africa’s Tim Clark, who carded a 68, and rookie Justin Thomas - another overnight co-leader who signed for a 70.
Max Homa was alone in seventh place on 199. Second-round co-leader Webb Simpson was part of a big group on 200.
That group also included South Korea's Kim Hyung-Sung, who had nine birdies in an eight-under 62.
Kim, who teed off on 10, closed his round with three straight birdies at seven, eight and nine, after his only bogey of the day at the sixth.
Walker admitted he was "pretty bummed" after falling short at Kapalua on Monday.
"But I got over it," he said. "It's golf and you've got to get over it because you've got to go play the next day.
"It was nice to not have so much time between tournament," said Walker, who shook off a bogey at the second to notch four birdies on the front nine.
His inward run included six more birdies, with only a bogey at the par-three 17th slowing him down.
"Coming in the stretch I was hitting it good," Walker said. "I was firing at that flag on 17... didn't quite catch it all. Still, just going for it, especially coming in."
Kuchar, who birdied two of his last three holes, said he hoped to put some pressure on Walker on Sunday.
"It's awfully impressive what Jimmy's doing," he said of Walker. "I'm looking forward to playing with him and seeing if I can push him along."
Leading third-round scores on Saturday in the $5.6 million USPGA Sony Open (USA unless noted, par-70):
194 - Jimmy Walker 66-66-62
196 - Matt Kuchar 65-63-68
197 - Brian Harman 66-67-64, Troy Merritt 66-64-67
198 - Tim Clark (RSA) 65-65-68, Justin Thomas 67-61-70
199 - Max Homa 69-67-63
200 - Jason Kokrak 67-69-64, Shawn Stefani 69-66-65, Harris English 66-69-65, K.J. Choi (KOR) 68-67-65, Gary Woodland 70-65-65, Scott Piercy 67-67-66, Camilo Villegas (COL) 63-70-67, Daniel Summerhays 66-67-67, Russell Knox (SCO) 66-65-69, Webb Simpson 62-66-72, Kim Hyung-Sung (KOR) 69-69-62
201 - John Peterson 65-70-66, Brian Davis (ENG) 66-70-65, Zac Blair 71-66-64, Ryan Palmer 69-63-69, Paul Casey (ENG) 62-70-69, Robert Streb 63-69-69
202 - Charles Howell 69-66-67, Nicholas Thompson 69-67-66, Jerry Kelly 73-62-67, Daniel Berger 68-66-68, Chez Reavie 67-67-68, Jason Day (AUS) 65-69-68, James Hahn 69-64-69, J.J. Henry 65-67-70
