Van Pelt, who has played all 36 holes, is 10-under 134.
About half of the field was still on the Quail Hollow golf course when play was stopped. The rain shower caused a two-hour delay, and play was halted one hour after it was resumed.
Van Pelt matched Kirk Triplett's 2004 course record -- and his 36-hole total of 134 topped the two-round record set by Tiger Woods, also in 2004.
Jim Furyk -- the 2003 U.S. Open winner, who had shared the first-round lead -- shot a 3-under 69 Friday to sit alone in second place at 7-under 137.
Davis Love III (69), the 1997 PGA Champion, is third at 6-under 138.