The second round was completed Saturday morning after five hours worth of weather delays Friday forced play to be suspended.
Lowery entered Saturday in a four-way tie for first with Pat Bates, Alex Cejka and Brett Quigley, who were already in the clubhouse, at 12-under par.
Lowery, the first-round leader, started Friday with a bogey at one but went 5-under over his next 10 holes. He elected to finish the 12th hole Saturday morning as he stood 67 yards from the green for his third shot to the par-5 hole.
He dropped that shot on the green and rolled in the birdie putt to claim first place by himself. He quickly extended that lead with another birdie at the 13th.
The 42-year-old was not done. He again rolled home back-to-back birdies from the 16th to stretch his lead to four strokes. His second straight 64 tied Joey Sindelar's 36-hole scoring mark of 128, which Sindelar set in 1987.
Steve Allan and John Morgan both posted rounds of 7-under 65 to move to 11-under-par 133, where they share fifth place. Michael Bradley, Robert Gamez and David Gossett are tied one stroke further back at minus-10.
Spike McRoy, the 2002 champion, is one of four players tied at 9-under-par 135.
The cut line fell at 3-under-par 141 with 77 players advancing to play the final two rounds.