Six-times champion Woods eagled the par-five 18th, his ninth hole of the day, en route to a seven-under-par 65 on the easier North Course, one of two layouts hosting the fourth US PGA Tour event of the season.
Back at a venue where he has always felt extremely comfortable, the 37-year-old American took advantage of the four reachable par-fives as he also carded six birdies and a lone bogey to finish at 11-under 133.
"I played well today. I drove the ball great and took advantage of the par-fives," Woods said after covering the par-five holes in a combined five under. "That's basically where the round could be had.
"But it's tough out there," he added after playing his final hole in a heavy downpour. "The greens became pretty soft, and they became pretty bumpy.
"I tried to hit every putt where it was just falling in and not having any putts coming back because they're a little testy from about two feet."
Little-known American Billy Horschel was alone in second after carding a 69 on the tougher South layout with compatriots Jimmy Walker (69) and double heart-transplant recipient Erik Compton (65) among a group of six bunched at eight under.
Britain's Ross Fisher, competing on the US Tour this year for the first time as a full member, briefly trailed Woods by just one shot at nine under but bogeyed two of his last four holes for a 71 to finish four strokes off the pace.
Most eyes, however, were firmly focused on the progress of Woods, who has won the Farmers Insurance Open six times at Torrey Pines, along with the 2008 US Open at the same venue.
Three strokes off the pace overnight after opening with a 68 on the South layout, Woods missed an eight-foot birdie putt on his opening hole, the par-four 10th.
However he recovered with birdies at the 14th and 17th, where he rolled in a 25-footer, to sit just two strokes off the early lead.
Woods then eagled the 18th, after hitting a superb second shot to six feet, to join Howell in a two-way tie at the top before forging three ahead with further birdies at the first and second.
A brilliant approach into the seventh, where his ball spun back and hit the flagstick before settling five feet away, set Woods up for another birdie but he bogeyed the par-four eighth after finding a fairway bunker off the tee.
However he immediately recovered by reaching the green in two at the par-five ninth and safely two-putting from 50 feet to record his sixth birdie of the day.
Woods has gone on to win 34 times out of 44 when holding at least a share of the 36-hole lead on the US Tour but he expected conditions at Torrey Pines to become increasingly difficult over the weekend with a forecast for more rain.
"We've got a long way to go and this golf course is not going to get easier with this rain," he said. "The rough is going to get sticky. It's a pretty tough course."
The cut fell at one-under 141 with former Major winners Angel Cabrera, Keegan Bradley, Yang Yong-eun and Stewart Cink among those missing out.
Phil Mickelson, a San Diego native who won the first of his three titles here 20 years ago, made the cut right on the number after bogeying his last two holes for a 71 on the South course.
"I've got some work to do on the weekend," said the American left-hander, a four-times Major champion. "I just don't quite feel great.
"I've thrown a lot of shots away on the greens, and my iron play hasn't been as good as it has been heading into the start of the year. It's just a fraction off."
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