Though he made the second-round cut by a stroke on Friday after carding a one-under-par 71 on the easier North Course, the world number one was badly out of sorts on a difficult day for scoring as he laboured to a 79 on the brutal South layout.
It was his worst ever score at the event, which he has won at Torrey Pines a record seven times, and ensured he would miss the third-round cut for the leading 70 players and ties, giving him the unwanted label of 'MDF' (made cut, did not finish).
His score matched the second worst of his professional career, and is eclipsed only by the 81 he shot in strong winds and driving rain in the third round of the 2002 British Open at Muirfield.
Woods, whose remarkable playoff win at the 2008 U.S. Open also took place at Torrey Pines, declined to speak to Golf Channel and CBS Sports after he had signed his scorecard, and also turned down requests to talk to reporters.
"I'm done," the 14-times major champion said before signing a few autographs for fans and then being driven away from the course in a van.
Woods, who won last year's Farmers Insurance Open by four shots in a fog-delayed Monday finish, endured a damaging run of back-to-back double bogeys followed by five straight bogeys from the 18th, his ninth hole, to finish at six-over-par 222.
That stumbling stretch ended with a welcome birdie at the par-four seventh, where he good naturedly removed his cap and bowed to the crowd, before closing with pars at eight and nine.
Woods chunked his chip from in front of the green at the par-five ninth, his ball ending up 10 feet short of the hole, but he sank the par putt to avoid shooting his first score of 80 or worse in the United States as a professional.
Despite competing at one of his favourite and most successful venues, Woods struggled in challenging, sun-baked conditions at Torrey Pines where the rough is surprisingly lush and the fairways are running firm and fast.
One under after eight holes, his day began to fall apart with his double-bogey at the 18th where he hit his second shot into water, took a penalty drop and dumped his fourth into the back greenside bunker.
Woods also doubled the par-four first, after three-putting, and then bogeyed the next five holes before sinking a five-footer for birdie at the seventh.
He chipped in to par the eighth, bringing a wry smile to his face, and saved himself the ignominy of an ugly 80 with his clutch putt for par on the ninth green.
Woods was playing in his first tournament since his playoff loss six weeks ago to Zach Johnson at the Northwestern Mutual World Challenge which he hosts in his native California.
His next event is the European Tour's Dubai Desert Classic next week, a tournament he won in 2006 and 2008.