Dufner shot a 7-under 65, matching the best round of the first two days on the Pete Dye-designed course that is being used in the tournament for the first time since it was dropped from the rotation after its 1987 debut.
''It's a difficult golf course,'' Dufner said. ''There's a little bit of room to play off the tee, but if you get off the path a little bit, you can get into some trouble. He's got some water out there. He's got some tricky bunkers. You get some uneven lies here and there. ... It's definitely the most difficult of the courses we have played here.''
Jamie Lovemark was a stroke back after a 65 on the adjacent Nicklaus Tournament Course.
Dufner parred the final four holes, escaping trouble on the par-5 16th after his drive strayed to the left. The 2013 PGA Championship winner played the front nine in 6-under 30, bogeyed the 10th after hitting into the greenside water, and added birdies on 12 and 14. He had only 22 putts, one-putting 11 of 12 greens in the middle of the round.
''The greens are of kind of difficult,'' Dufner said. ''They run on some angles and there's some slope.''
Dufner was forced to lay up on all four par-5 holes and took advantage of many short approach shots.
''Any time I'm inside of 130 yards I feel pretty good,'' Dufner said. ''I had some really good numbers with my wedges, which helps. I wasn't in between on too many of them. I could go ahead and hit a full sand wedge or a full gap wedge a couple times.''
Dufner's drive on 16 perched on a ledge of dormant grass above one of the deep bunkers that line the left side. The ball at knee level, he slashed it 100 yards down the fairway before slipping to his hands and knees on the steep bank.
''I was a little disappointed with that,'' Dufner said. ''I thought I would have a good go at that green in two and maybe get another birdie or possibly even an eagle and walked away with a five, but no damage done.''
Dufner had a 15-under 129 total. Coming off a ninth-place tie last week in Honolulu in the Sony Open, he opened with a 64 on Thursday on the Nicklaus Course. He will play La Quinta on Saturday, and return to the Stadium Course for the final round Sunday.
Lovemark holed out from 105 yards for eagle on the par-4 first, his 10th hole of the day.
''Got a little tired coming down the stretch,'' Lovemark said. ''There's some long rounds out here.''
Bill Haas, the winner in 2014 and 2015, was three strokes back along with Jason Gore, Anirban Lahiri, Andrew Loupe and Adam Hadwin. Haas shot 66, Gore 64, and Lahiri 68, all at the Nicklaus Course. Loupe had a 66 on the Stadium Course, and Hadwin a 66 at La Quinta.
Phil Mickelson was 11 under in his first start since the Presidents Cup in October and first since splitting with swing coach Butch Harmon to work with Andrew Getson. The 45-year-old Mickelson had a 65 on the Nicklaus Course.
''I'm probably a week away, if I'm being honest,'' Mickelson said. ''But I've also won with a lot less game than I have right now. I still expect to get in contention and have a good weekend, but a lot of iron shots are 12, 15 feet off.''
The 2002 and 2004 champion is winless since the 2013 British Open.
DIVOTS: The Stadium Course had a stroke average of 70.218 for a two-day mark of 71.029. The Nicklaus Course has averaged 69.145 overall, and La Quinta 69.328. ... Chesson Hadley made a double-bogey 5 on the island-green 17th on the Stadium Course after trying to hit out of the rocks and going into water, then holed out from 142 yards for eagle on 18. He shot 73 and was tied for 113th at 2 under. ... Nick Taylor had a hole-in-one on the 205-yard sixth on the Stadium Course. He was tied for 70th at 5 under after a 69. ... Patrick Reed, the 2014 winner, was tied for 54th at 6 under after a 69 on the Nicklaus Course.