GREENSBORO, August 17, 2014 (AFP) - Watney, who won the last of his five US PGA Tour titles at the 2012 Barclays, had a 54-hole total of 14-under par 196 at Sedgefield Country Club.
Canada's Fritsch, who also signed for a 65, was a stroke back on 197.
Sweden's Freddie Jacobson fired a 66 to join overnight co-leader Heath Slocum on 198. Slocum slipped back with a two-under 68.
Slocum needs a third-place finish in the US tour's final regular-season tournament to qualify for the FedExCup playoffs, which start next week with the Barclays.
Scott Langley, who was tied with Slocum after 36 holes, managed a one-under 69 and slipped into a tie for fifth on 199.
Brandt Snedeker, the 2007 champion, and 2011 winner Webb Simpson both shot 66s to join Langley.
After two birdies in the first nine holes, Watney added three more birdies coming home, capping his round with a birdie at 18 that took him past early pace-setter Fritsch.
Fritsch also played without a bogey, his round highlighted by an eagle two at the par-four eighth.
Fritsch goes into the weekend seeking his first US tour title -- and a rise from 163rd in the FedEx Cup standings into the top 125 who advance to the playoff series.
Argentina's Andres Romero had the best round of the day, a 64 that put him in a group of six players on 200. That group also included Scotland's Martin Laird and first-round leader Camilo Villegas of Colombia.
"I kept it pretty simple," Watney said. "The part I liked most that was that down the stretch I had to make a few putts, and I was able to do it. I'm in the arena. I love to have a chance."
Watney, 33, had a steady start with a pair of pars preceding a 10-foot birdie putt on the par-three third.
He parred his next four, then landed his approach inside two feet at the eighth.
After birdies at 13 and 15, he closed his round by rolling in a 19-foot birdie putt at the last.
Fritsch's round was highlighted by his eagle at the eighth, where he holed a wedge shot from 76 yards out.
He poured in a 57-footer for birdie at 14.
Leading third-round scores on Saturday in the US PGA Tour $5.3 million Wyndham Championship (USA unless noted, par-70):
196 - Nick Watney 67-64-65
197 - Brad Fritsch (CAN) 69-63-65
198 - Freddie Jacobson (SWE) 68-64-66, Heath Slocum 65-65-68
199 - Brandt Snedeker 68-65-66, Webb Simpson 64-69-66, Scott Langley 65-65-69
200 - Andres Romero (ARG) 70-66-64, Bill Haas 68-66-66, Kevin Kisner 69-64-67, Camilo Villegas (COL) 63-69-68, Bo Van Pelt 67-65-68, Martin Laird (SCO) 65-66-69
201 - Ricky Barnes 66-69-66, Will Wilcox 67-67-67, Jhonattan Vegas (VEN) 67-65-69, Andrew Svoboda 67-64-70
202 - Roberto Castro 71-66-65, Josh Teater 67-69-66, Jason Allred 69-66-67, Robert Streb 69-66-67, Justin Bolli 67-68-67, Paul Casey (ENG) 65-69-68, DA Points 67-65-70, Brian Stuard 66-65-71
203 - Stuart Appleby (AUS) 68-69-66, Bae Sang-Moon (KOR) 69-68-66, Doug LaBelle 72-65-66, David Toms 67-69-67, Tim Clark (RSA) 67-67-69, Scott Piercy 70-64-69, Johnson Wagner 66-67-70, Andrew Loupe 65-68-70, William McGirt 64-68-71, Carl Pettersson (SWE) 67-65-71