Billy Hurley, who fired a 5-under 65 at the Pittsburgh Field Club on Tuesday, shared second place with Trip Kuehne -- the 1994 runner-up to Tiger Woods.
Holmes notched eagles at the par-5 11th, his second, and the par-5 fifth. He also birdied the par-5 15th, but stumbled to bogeys at Nos. 18, 2 and 8.
Kuehne posted an even-par 70 at the famed Oakmont Country Club, where only one player broke par during the two rounds of stroke play.
Camilo Villegas and Brock MacKenzie shared fourth place at even-par 140. First-round leader Ryan Moore struggled to a 6-over 76 at Oakmont. He dropped into a tie for sixth place at 1-over-par 141. He was joined there by Jay Reynolds, Bruce McDonald, Gregg Jones and Steve Bendt.
Among the other notables advancing to the match play portion of the event are Bill Haas (3-over-par 143), Mike McDermott (5-over-par 145) and Tom Glissmeyer (6-over-par 146).
The first round of match play begins Wednesday, but not before a playoff between 14 men determines the final 12 spots in the field of 64.
Luke List, one of the top players entering the event, struggled to a 10-over-par 150 was one of the casualties of the stroke play portion. Also not advancing to the match-play portion was local favorite Sean Knapp, of Oakmont, who posted back-to-back rounds of 8-over 78
Oakmont, the site of seven U.S. Opens and this its fifth Amateur championship, is where the six rounds of the match-play portion of the event will be staged.
The 36-hole final is scheduled for Sunday.