Woods, who underwent back surgery last year, was in obvious discomfort from the outset of his round after being forced to sit and wait out a lengthy fog delay.
The 14-time major winner, who continued to struggle with his swing and short game, was two over par on the North course when he decided to pull out, his third withdrawal in his last nine starts.
Woods was due to start his round after an already lengthy delay on Thursday morning (local time) before more fog rolled over the coastal course, causing a suspension in play.
"When we had that break, it (the back) just never loosened back up again," Woods told reporters. "And when we went back out, it just got progressively tighter.
"It's frustrating that it started shutting down like that. I was ready to go. I had a good warm-up session the first time around.
"Then we stood out here and I got cold, and everything started deactivating again. And it's frustrating that I just can't stay activated."
Woods, who has won eight tournaments at Torrey Pines, including a U.S. Open, was taken straight from the course to the car park where he told reporters he had failed to get his gluteus maximus muscles warm.
"It's just my glutes are shutting off," the 39-year-old said. "Then they don't activate and then, hence, it goes into my lower back.
"So I tried to activate my glutes as best I could, in between, but they never stayed activated."
Less than a week removed from shooting a career worse 82 in Phoenix, Woods started poorly out and was clearly in some pain.
He continued to fan shots way right and while his short game had some good moments, for example he chipped in for par on the second hole, it also caused him problems. On the first hole, he bladed a chip across the green on the way to a bogey.
