Woods was preparing to putt at the seventh green at CordeValle -- his 16th hole of the day -- when the man burst out of the crowd and tossed the hot dog in Woods' direction.
Woods backed away from his putt and the man promptly surrendered to tournament security personnel and police.
Authorities did not give the man's name, but said he appeared to be intoxicated and had been arrested.
While 14-time major champion Woods has had to endure the occasional heckler since his return to competition in 2010 in the wake of a sex scandal, he had never had a spectator get through the ropes to approach him.
"When I looked up, the hot dog was already in the air," said Woods, who regretted missing his subsequent birdie putt but otherwise didn't seem especially concerned. "He was pretty far away from me."
Woods said the man "laid on the ground and looked like he wanted to be arrested because he ... put his hands behind his back and turned his head."
"I guess he wanted to be in the news," Woods said. "And I'm sure he will be."
Australian Rod Pampling, playing in the same group with Woods and India's Arjun Atwal, called the incident "bizarre".
Atwal noted that it was lucky the incident didn't turn uglier.
"They could have shot him," Atwal said. "The cops could have thought it was something else."
"He's just an idiot," Dan Diggins, the tournament's director of security, said of the man, although by the time Woods' round was finished Diggins could see the lighter side.
"It wasn't a chili dog -- that could have been bad," he said.
Woods, the former world number one who was making his first start since missing the cut at the PGA Championship in August, notched his third straight three-under 68.
Playing in the first group of the 10th tee, he got off to a blazing start with birdies at 10, 12, 14 and 15 before dropping a stroke at the par-three 16th.
He birdied the par-four 17th, but slowed down with bogeys at the second and fifth after making the turn, although he capped his round with a birdie at the par-five ninth.
Woods' four-round total of seven-under 277 had him stuck firmly in the middle of the pack.
The good news for Woods was that for the first time since the 2010 Deutsche Bank Championship he notched three straight rounds in the 60s.
"I got better every day, and unfortunately, a couple times I didn't get the momentum going when I had a couple of chances to make putts," Woods said. "I could have just really got it rolling."
Woods put that down to lack of tournament play. Since injuring his left leg at the Masters in April Woods has played only 10 complete rounds.
He hosts an event at Pebble Beach next week to raise money for his charitable foundation and will play a few more exhibitions before he tees it up at the Australian Open November 10-13, a week before the Presidents Cup match play showdown between the United States and an international team.