The former U.S. Amateur champion shot 5-under 65 at the water-laden Bethpage Black golf course in New York and led Lucas Glover (64) by one shot. He broke the record of 133 for 36 holes set in 2003 by Jim Furyk and Vijay Singh.
"Obviously at the beginning of the week you didn't think that score was out there (but) it's pretty cool," the 28-year-old native of Stockton, Calif., said.
His second round included nine birdies and one bogey. Glover held the lead Friday when play was suspended by darkness.
Former Masters champion Mike Weir, the first-round leader, shot even-par 70 Saturday and was alone in third place at 6-under 134.
Defending Champion Tiger Woods shot 1-under 69, but at 3-over 143, he trailed by 11 shots and barely made the 4-over 144 cut line. Among those missing the cut were former major winners Padraig Harrington (152) and Ernie Els (155).
The tournament was suspended Saturday before the third round got started. Tournament officials hope to resume play early Sunday.