Snedeker, the Nationwide Tour grad who equaled the Torrey Pines North Course record with a 61 Thursday, is now at 13-under-par 131. He played the tougher South Course in the second round and posted four birdies and two bogeys.
Further back, Woods sits tied for 12th place at 6-under 138 after posting a 72 on the South Course.
In his first tour event of the season, Woods opened with a 66 in the first round. On Friday, he mixed three birdies with three bogeys.
'I felt comfortable with my swing,' Woods said. 'I hit a couple of loose ones here and there, but the greens are unpredictable.'
Woods hit two 'loose' shots at the par-5 18th.
Using a wood out of a fairway bunker, he topped his second shot and nearly had it roll into a pond. He then knocked his third shot into a bunker behind the green, finally making par after blasting to within 8 feet.
'The second shot (in front of the pond) was the worst. If I can't hit the green from 59 yards, that's not good,' Woods said.
He's seven shots back, but Woods is used to this position at the Buick: It's the same size deficit he overcame on the weekend to win last year, and two strokes better than the one he erased to win in 1999.
In fact, Woods has never led through 36 holes in any of his four wins at this event. If he can figure out the greens -- he ranks 40th in putting -- another comeback is probable.
But 'the greens are very interesting,' Woods sighed. 'Don't leave yourself short putts around here.'
Looking at Snedeker's stats, it's hard to imagine he holds a three-shot lead -- especially since he's hit only a quarter of Torrey Pines' fairways through two rounds.
Friday, his number was even worse than that: just 21 percent.
'I didn't drive it very well today at all. I don't know how many fairways I hit, but probably wasn't too many,' he said.
Snedeker has been saved by his scrambling and putting -- he's top-5 in both -- and his play has been buoyed by a supportive gallery that showed up to see the youngster who flirted with 59 Thursday.
'[It was like] nothing I've ever experienced before,' said Snedeker, 26. 'They were rooting me on and it really kind of got me around the last five or six holes.'
Phil Mickelson had a bogey-free 66 on the North Course to stay above the cut line, finishing the day at 4-under 140. He opened with a 74 Thursday on the South Course.
The cut line fell at 3-under 141.
'It was a change in the courses,' Mickelson explained his improvement from Day 1.
'I'm a little rustier than I thought I would be starting out (the season),' he continued. 'What is happening is my distance control isn't good.'
Players will be on the South Course for the final two rounds. Through Friday, it was playing around four shots harder than the North Course.
'Certainly, it's a lot harder,' Mickelson said.
Among those missing the cut were the last two players besides Woods to win this event: John Daly and Jose Maria Olazabal (both 144).