Woods carded a second-round 73 for an even-par total of 144, one shot outside the cut line of one-under 143. It marked the eighth time as a pro Woods has missed a cut -- and the second time he has missed it at this event.
Woods struggled with his accuracy off the tee but really suffered on the greens, needing 33 putts in his round.
Long before the cut was official, Woods was resigned to an early exit. "This is one of my favorite tour stops, and unfortunately, I'm just not going to be around for the last two days," said Woods, who won at Quail Hollow in 2007.
Woods missed the cut here in 2010, not long after he returned to golf in the wake of the sex scandal that rocked his personal life.
American Nick Watney was the halfway leader after a 64 for 12-under 132. Webb Simpson posted a 68 for sole possession of second place on 133.
Woods, whose tie for 40th at the Masters was his worst ever finish at Augusta National as a professional, again could not capitalize on good scoring conditions early in the day.
He failed to birdie any of the par-fives and said that as at the Masters, he allowed old habits to creep in and disrupt the new swing he has put together under the guidance of coach Sean Foley.
"It's just that I get out there and I want to get comfortable, and I follow my old stuff," he said. "I know what I need to do. It's just I need more reps doing it."
In an odd twist to the 14-time major champion's day, Woods was awarded a free drop after a fan apparently walked off with his ball at the par-five fifth, where Woods went over to the gallery as he tried to reach the green in two.
When Woods walked up, his ball was nowhere to be found.
Tour official Mark Russell spoke to several people who saw the ball land and determined that someone took it.
He allowed Woods a free drop at the spot where spectators said they saw it.
"There were about five or six people that ran over to the ball, and the next thing you know, we get down there and there's hundreds of people and no ball," Woods said.
"We looked around for a while, and then Mark came over there and analyzed the situation and what was going on."
Australian Geoff Ogilvy, playing in the same group with Woods and Simpson, agreed with the general consensus that the ball had been taken.
"It got picked up for sure. There can't be any doubt," Ogilvy said. "I guess there's a chance it could roll under the pine straw, but not when 500 people are there looking for it.
"Usually, Tiger's ball, they all circle around and stare at the ball. And it was gone."
Woods is enduring an erratic 2012 season. He withdrew in the final round at Doral with a sore Achilles tendon, then won at Bay Hill to claim his first PGA Tour title in more than two years.
That victory sent him into the Masters on a high, but he was not a factor at Augusta and drew stern criticism for a burst of temper in which he kicked a club after a poor tee shot.
Woods said he would just keep practicing. "The entire week, I didn't play the par-fives well," Woods said. "Today I made four pars. You just can't do that, especially when all of them are reachable with irons. I didn't take care of the par-fives, missed a couple other little short ones for birdie, and consequently got no momentum during the round."