First-round leader Dave Rummells managed an even-par 72 in round two. He was joined in second place at minus-6 by Craig Bowden (68), Charlie Wi (71), Nick Malinowski (67) and Andrew Pratt (68).
Last week's surprise playoff winner Kyle Reifers fired a 5-under 67. He jumped into a share of seventh at minus-5 alongside David Mathis.
Bad weather Thursday forced the completion of round one into early Friday. The back up was no problem with Friday's nice weather as both the first and second rounds were completed.
Dufner came flying out of the gates with birdies on one and two. He dropped a stroke on the par-3 fourth at Peek 'n Peak Resort's Upper Course though.
The 29-year-old bounced back with a birdie on No. 6 to get back to 6 under.
Dufner, who collected his second tour win earlier this year at the LaSalle Bank Open, then birdied the seventh.
'The course conditions here are pretty similar to Chicago and the Open,' Dufner said in reference to the LaSalle Bank Open and the U.S. Open. 'The mindset is the same in that you have to hit it in the fairway if you want to have a chance to score.'
Dufner ran off nine straight pars before a birdie on 17 gave him the outright lead.
'I might have been a little bit rusty after taking a week off. After playing well in Chicago and halfway decent at the Open (T-40), I'm playing with a lot of confidence right now,' admitted Dufner. 'After playing in the Open, the fairways seem wider here and the greens seem bigger here. Everything seems a little easier.'
Rummells, a two-time winner on the Nationwide Tour, traded a birdie for a bogey from the fifth. He got to 7 under with a birdie at the par-4 eighth. After bogeys on the 12th and 13th, Rummells got back within one of the lead thanks to a birdie on 16.
Bowden opened with a birdie on the 10th. He collected two bogeys and two birdies the rest of his opening nine to turn at 3 under. On the front nine, Bowden posted back-to-back birdies from the second and again from the eighth. In between however, he tripped to a bogey on five to share second.
Wi played the back nine first and parred his first eight holes. He then birdied three of his next four to get to 8 under. The 34-year-old bogeyed the next three to tumble to 5 under. Wi got one stroke back with a birdie on the eighth.
Malinowski notched three birdies and a bogey on his opening nine. On his second nine, the front side, he carded four birdies and a bogey to move into a tie for second place.
Pratt started with three straight birdies from the first. He faltered to a bogey on five, but got that stroke back with a birdie at No. 9. Pratt's lone birdie on the back nine came at the 14th. He parred the other eight holes around the turn.
Michael Bradley, Gavin Coles, Glen Hnatiuk, John Merrick, Michael Putnam, Jeff Quinney and Steve Wheatcroft share ninth place at 4-under-par 140. Defending champion Esteban Toledo is one of 12 players a shot back at minus-3.
The cut fell at even-par 144 with exactly 60 players moving on to the weekend.