Pernice fired a 7-under 63 over the Congressional Country Club course for a two-day total of 131. Jeff Overton matched that 36-hole total by shooting a 65.
Cliff Kresge and Anthony Kim shared third at 134. First-round leader Steve Marino was one of seven players at 135.
Pernice, with two PGA Tour victories to his credit, played a bogey-free round.
"I hit a lot of iron shots in there close and I had a couple of 20 footers that were the bonuses," Pernice said.
Defending champion K.J. Choi was at 139.
It took a score of 143 to make the cut. Among those missing it was Masters champ Trevor Immelman (144).