Playing the tougher Stadium Course, the 2010 American Ryder Cup player carded eight birdies, with a solitary bogey, to move to 15 under par.
Dufner started the day as joint leader on eight under and made hay on the front nine, peppering his card with birdies at holes one, two, five, seven, eight and nine.
It leaves him one shot clear of Jamie Lovemark, who carded a 65 on the Tournament Course. The American was helped by an eagle on the par-four first and five birdies.
Five men are a shot further back on 12 under, including Jason Gore, whose eight-under 64 on the Tournament Course was the best round of the day.
Another man climbing the leaderboard was Phil Mickelson, whose 65 on the Tournament Course saw him surge up 24 places to be tied eighth on 11 under.
It was a disappointing day for joint overnight leaders Jeff Overton and Jerry Kelly. Overton's one-under-par 71 saw him slip down to tied 19th on nine under while Jerry Kelly struck a 70 to move to 10 under.