Woods retired on the 13th hole at PGA National, where he was five over par for the day and level for the tournament, having struggled to the turn in five-over 40.
"It's my lower back with spasms," Woods, 38, said in a statement. "It started this morning warming up."
He said it was the same feeling he had during The Barclays tournament last August, where he finished in obvious discomfort.
His withdrawal comes less than six weeks before the first major of the year, the Apr. 10-13 Masters at Augusta National.
Woods, whose career major tally of 14 is second only to Jack Nicklaus, said it was too soon to know whether he would be able to defend his title at the WGC-Cadillac Championship, starting in Miami on Thursday.
"It's too early to tell," he said. "I need treatment every day until Thursday to try to calm it down and we'll see how it is."
Woods last withdrew from a tournament at the 2012 Cadillac Championship, citing an Achilles injury which did not prove to be serious. He bounced back two weeks later to win the Arnold Palmer Invitational.
His early exit from the Honda Classic on Sunday was probably a precaution more than anything else, and it would be premature to speculate that his back will hinder his preparation for the Masters.
Nevertheless, the recovery period from back injuries is notoriously unpredictable.
"If you're hurting, you don't need to risk injuring yourself even more," said Luke Guthrie, who played with fellow American Woods for the last two rounds at PGA National.
"He's had his share of problems with injuries (so) there's no reason to chance it."
Guthrie observed that Woods hit a couple of uncharacteristic shots during the final round.
"The drive on three was the first I noticed he wasn't feeling the greatest (but) I didn't think much of it maybe until 11 (where) I noticed he was bending down gingerly," he said.
Guthrie felt that Woods had given maximum effort.
"He was battling out there," he said. "It's not like he was throwing in the towel."
Woods has competed in only one other event on the 2013-14 PGA Tour, failing to make the 54-hole secondary cut at the Farmers Insurance Open in January.
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