The former world number one, a six-times winner of the event at the San Diego course, birdied three of his first seven holes to move to 17 under overall when play was suspended for the day in fading light.
Fellow American Nick Watney, winner here in 2009, was tied for second, after eight holes, with defending champion Brandt Snedeker, who had completed 13.
Burly Canadian Brad Fritsch, a US Tour rookie at the age of 35, was a further two strokes back at nine under after seven holes.
However, Woods was in full command at one of his favourite venues in his bid to win a third different PGA Tour event for a seventh time. He has already recorded seven victories apiece at the WGC-Bridgestone Invitational and the Arnold Palmer Invitational.
"I played well today," a smiling Woods told reporters. "Overall, I'm very pleased that I was able to build on my lead. As of right now, I've got a six-shot lead, so that's a positive.
"I've got to continue with executing my game plan. That's the idea. I've got 11 holes to play, and I've got to go out there and play them well."
Woods was delighted with his game.
"It's probably the whole package," the 14-times major champion said when asked which aspect of his game had contributed most to his 17-under total after 61 holes at Torrey Pines.
"I've driven the ball well, I've hit my irons well, and I've chipped and putted well. Well, I've hit good putts. They all haven't gone in.
"Today certainly you're just trying to get your speed right, because it was wobbling all over the place," Woods said of greens that became increasingly bumpy during the afternoon.
Woods is so far 11 under on the par-five holes this week at Torrey Pines, a noted strength of his game during his prime. While driving the ball considerable distances here, he has also been surprisingly accurate.
"I just drove it on a string all day, at least all morning," he said of his form off the tee during his three-under-par 69 in the third round. "I hit the ball pretty good. It seemed like I was always in pretty good position."
His rivals are well aware of his stellar overall track record on the U.S. circuit where he has gone on to win 49 times out of 53 when holding at least a share of the 54-hole lead, including 14 of 15 in the majors.
So far this week, he has dominated a medium-strength field at the PGA Tour event which began with 17 players ranked in the world's top 50.
"I've got to make some more birdies," said FedExCup champion Snedeker, who came from seven strokes behind in the final round last year to win the title in a playoff. "I've got a long way to go.
"I've got a guy at the top of the leaderboard that doesn't like giving up leads, so I have to go catch him."
Four strokes in front when the weather-delayed third round was completed earlier in the day, Woods did well to scramble pars on the first two holes after missing both fairways badly to the left.
As the late afternoon shadows lengthened in soft sunlight, the world number two hit a superb tee shot to 10 feet at the par-three third and rolled in the birdie putt to regain a four-shot cushion.
Woods then conjured an outrageous birdie at the par-four fourth after his ball ended up behind a tree to the right of the fairway following another wayward tee shot.
Having considered his options, he cut a low second shot around the tree to just short of the green before chipping in from 40 feet for a miraculous three to forge five strokes clear.
Woods also birdied the par-five sixth, rifling an exquisite 232-yard second shot from the right rough to 28 feet and comfortably two-putting to move six ahead.
He then found the right fairway off the tee at the seventh before the siren sounded to halt play for the day and, with the option to complete the hole, struck his approach to 30 feet and safely two-putted for par.
Woods began a marathon day at Torrey Pines two strokes in front of the chasing pack after thick fog had allowed only five minutes of play on a frustrating Saturday at the coastal venue.
Looking sharp in every component of his game, he revived memories of his former dominant self as he doubled that lead by shooting a three-under-par 69 in the third round.
At one point a commanding six shots ahead, Woods bogeyed the par-five 18th after finding a poor lie in a fairway bunker off the tee and a greenside bunker with his third shot to finish four ahead of Fritsch (70).
Double heart-transplant recipient Erik Compton was a further stroke back after eagling the last for a 71 while Watney (71) was among a group of five players knotted at eight under.