Flesch, seeking his second victory in two months, was at 19-under 197, tying the PGA TOUR's lowest 54-hole score in relation to par this year. Pettersson (66) briefly tied for the lead after consecutive birdies on the back nine, but Flesch rallied with four of his own over the final five holes to keep the top spot to himself.
Warren (68), who finished second to Flesch at Reno in early August, birdied his final hole to tie Pettersson for second. They were two shots in front of Parker McLachlin (65). Michael Allen (68) and Bill Haas (69) were another stroke back at 12 under.
Justin Leonard and Sean O'Hair shot 66s and were tied at 11 under with Jarrod Lyle (68), John Mallinger (68), Joe Ogilvie (68), Bart Bryant (69), Johnson Wagner (69), Craig Bowden (70), Mathew Goggin (70), and Charley Hoffman (71).
Jeff Gove, who started the day tied with rookie Brendon de Jonge one shot behind Flesch, faltered with a 4-over 76 and was out of contention 10 shots back.
De Jonge, a rookie playing a weekend for only the seventh time in 20 events, was paired with Flesch, and it didn't take long for de Jonge to run into trouble. He made bogey at the par-4 second hole after hitting into a greenside bunker, fell back to 10 under after another bogey on the next hole, and finished with a 75.
Flesch rolled in a 17-foot birdie putt on the second hole, chipped to inside a foot for birdie on the par-5 fifth hole, and hit to within 7 feet at the par-3 sixth hole to set up another birdie that put him at 16 under, three shots ahead of Goggin and Gove.
Flesch finished the front nine with three straight pars, including the ninth, where he had made double bogey and bogey the first two rounds. He bogeyed the par-3 11th hole, driving to the left of the green and then flubbing his approach, two-putting from 23 feet, and Pettersson took advantage.
Four shots behind at the start of play, Pettersson began his charge early, hitting a 7-iron to 12 feet and making eagle at the par-5 fifth hole to reach 12 under. He made birdie at No. 13, hitting a 7-iron to 15 feet, and another at the par-3 16th hole with a clutch putt from 20 feet to move within a shot of the lead. He followed that by hitting a gap wedge to 11 feet and making another birdie at No. 17 for a share of the lead at 15 under.
It didn't last long.
Flesch regained his touch after two pars, reeling off three birdies in a four-hole span, making a 20-foot putt at No. 17 to open a three-shot lead.
The first two rounds were played under ideal conditions -- sunny skies and temperatures in the 80s and very little wind. On Saturday, the sun was still out and it was warm again, but a stiff wind that reached as high as 25 mph made the 7,482-yard Atunyote course a little more challenging.
It didn't have much of an effect on the 48-year-old Allen, though. He stayed out of trouble until the final hole, hitting 13 of 14 fairways and reaching 14 of 18 greens in regulation.
At the 610-yard, par-5 18th, however, he drove off course to the right, his second shot left him 256 yards from the pin, and he two-putted from 18 feet for bogey.
'That's all I really wanted the end of the week, a few shots back and got a chance,' said Allen, who last year made his 13th trip to the Q-school finals and earned his PGA TOUR card for a record ninth time. 'It's a nice change to be in the hunt.'