Rolling the ball beautifully on the greens, Dufner began with a pair of birdies, bagged another at the fifth, and closed his opening nine with a run of three straight to reach the turn at six-under 30.
His only bogey came at the 10th but he carded two more birdies at 12 and 14 to post a 15-under total of 129.
Dufner took just 22 putts in his round at the challenging PGA West's TPC Stadium Course, one of three layouts used in the tournament.
One stroke back at 130 was fellow American Jamie Lovemark, who matched Dufner's 65 thanks to an early birthday gift at the first, his 10th hole of the day, where he holed out from the fairway on the Nicklaus Tournament Course for an eagle-two.
"Made that shot from 105 yards. Nice little present," smiled Lovemark, who celebrates his 28th birthday on Saturday.
Five players were bunched at 12-under, three shots off the pace, including India's Anirban Lahiri (68), Canadian Adam Hadwin (66) and Americans Jason Gore (64), Andrew Loupe (66) and defending champion Bill Haas (66).
Another stroke back was five-times major winner Phil Mickelson, who returned a 65 and said that despite a belated start to his season he was nearing top form.
"I'm probably a week away," he said. "But I've also won with a lot less game than I have right now, so I still expect to get in contention and have a good weekend.
"A lot of the iron shots are 12, 15 feet off. I know when I get it right I'll have a lot more tap-in birdies in the round."
(Reporting by Larry Fine in New York; Editing by Peter Rutherford)
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