Taking advantage of near-perfect conditions at the pro-am event long known for its low scoring, Dufner posted a 23-under total of 193 to finish two ahead of compatriot Jamie Lovemark, who carded a 65 at the PGA West's TPC Stadium Course.
Canadian Adam Hadwin was alone at 20 under after returning a 64 on the Jack Nicklaus Tournament Course, with Swede David Lingmerth a further two strokes back after a blistering 62 at La Quinta.
Dufner has not won on tour since capturing the 2013 PGA Championship, but he moved within one strong round of ending his drought when he mixed three birdies with two bogeys on his outward nine before catching fire after the turn.
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Hitting pinpoint approaches and putting superbly, the 38-year-old picked up further shots at the first, third, fourth, fifth, sixth, seventh and the ninth to double his overnight lead.
"I told the guys (his playing partners) that I was going to have a good back nine ... that I was about to do something good and it happened," Dufner told Golf Channel.
"When you start thinking like that, good things happen so that's just kind of where my mindset is right now. It helps when you are shooting 30s and 29s obviously, which I've done a couple of times this week.
"I'm playing good. I'm not in any trouble, I feel relaxed out there. I never feel like this has to happen or that has to happen. I'm just playing golf like you should."
Twice former champion Phil Mickelson, competing in his first event since last October's Presidents Cup, carded 66 to trail by six shots.
(Reporting by Mark Lamport-Stokes in Los Angeles; Editing by Andrew Both)
