Pernice shot a 7-under 63, the lowest round of the tournament by two strokes, to tie Nathan Green for first place at 8-under 132.
With low rounds being shot throughout the day at the Waialae Country Club, Pernice played the front nine in 4-under. He then made a 30-foot birdie putt at the par-4 15th and closed out his round in spectacular fashion.
Pernice has won twice on the PGA Tour, but not since the now-defunct International Tournament in 2001. Green is in his fourth season on the circuit without a victory.
First-round leader Shigeki Maruyama and Brian Gay were tied for third at 133. Former Masters champion Zach Johnson was alone in fifth at 134 while Geoff Ogilvy led the group at 135.
Ogilvy won last week's season-opening Mercedes-Benz Championship on the island of Maui.
It took a score of 1-over 141 to survive the 36-hole cut in the first full-field event of this year's PGA Tour. Among those missing the cut was recently-named 2010 U.S. Ryder Cup captain Corey Pavin.
Boo Weekley, one of last year's American Ryder Cup heroes, was one of those tied with Ogilvy for sixth place.