Woods shot even-par 70, walking off the course at 1 under par with a share of the halfway lead with Jim Furyk and David Toms. Toms had a chance to take the lead by himself with a birdie at No. 18, but left the putt a foot short.
Furyk went out early, shooting 69 to establish the clubhouse lead.
In the afternoon wave, Woods briefly held the lead alone before falling back into a first-place tie.
Phil Mickelson birdied the final hole to finish at 7 over and continue to the weekend.
World No. 1 Luke Donald and defending U.S. Open champion Rory McIlroy failed to make the cut, marking the second time in the last four majors the top two players in the Official World Golf Ranking did not advance to the weekend. Donald shot a 72 after an opening 79 and McIlroy followed his first-round 77 with a 73.