Tom Lehman, who battled with Woods down the stretch, missed a short par putt on 18 that dropped him into a tie for second place and cost him close to $170,000. Lehman, the American Ryder Cup captain, shot a 1-over 73 and shared second place with Charles Howell III (72) and Luke Donald (73) at 13- under-par 275.
Despite the three-stroke margin, Woods had to earn win No. 41 on the PGA Tour.
Woods and Lehman were tied at 15 under par when the duo reached the tee at the par-4 17th at the South Course at Torrey Pines. Both players found the fairway, but Woods stiffed his approach inside 5 feet. Lehman landed in the bunker on the right side of the green.
Lehman's bunker shot hopped over the hole and ran 15 feet past the hole. He missed the putt to fall one back of Woods, who seemed poised to extend his lead. Woods pushed his putt right, so Lehman had a chance at the par-5 closing hole.
Once again both players found the short grass with their drives. Lehman had a 262-yard carry over water, but decided to lay up short of the pond and make birdie from there. Woods went for the putting surface in two, but hit a poor shot that came to rest right of the pond.
Lehman did not hit his best wedge and his ball bounced back into the rough short of the green. Woods chipped his third 15 feet right of the hole, then sealed the tournament when his birdie putt fell into the cup.
'That was a great win,' said Woods, who won this tournament for the third time. 'It was a tough battle and I hung in there as best I could. It's a nice way to start out the year.'
Woods endured a sub-par year in 2004 as his only victory came at the WGC- Accenture Match Play Championship. It took only two starts in 2005 for Woods once again to find the winner's circle.
'I felt like I had a chance at Mercedes, I just wasn't putting very good,' said Woods, who pocketed $864,000 for the win. 'This week the putter came around and I hit it decent.'
Woods also benefited from some bad breaks that plagued his runners-up.
Lehman bogeyed his final two holes to lose out on his first win since the 2000 Phoenix Open. He carded a 1-over 73 in the final round and settled for his best finish since last year's stop in Las Vegas.
Donald, who lost in a playoff to John Daly in 2004, held a two-shot lead through 12 holes Sunday. The problem came at 14 as his approach went long and left into a hazard. He did no better than double bogey, but had some more chances down the stretch.
Donald drove out of bounds on the left side at 17. He converted a long putt just to save bogey, but he was out of contention for his second PGA Tour title.
'I let it slip at the end,' said Donald. 'I was trying out there on every shot. A couple of bad swings - it's unfortunate. I still need to do a little work.'
Howell finished several groups ahead of Woods and Lehman. At the 18th, Howell took an aggressive line at the flag and his ball hit the stick and bounced back into the water. His fifth shot came up short of the green in the rough, but he chipped in for bogey.
Several fog delays pushed the tournament back and Woods and Lehman played 32 holes on Sunday.
Perhaps that helped the 29-year-old Woods. In the final round, he birdied the second hole, then missed the green with his second at the par-5 sixth. Woods chipped to 10 feet and sank the birdie putt, then converted a 15-footer for birdie at the eighth.
Woods found the right bunker at the 11th, and made bogey to fall two behind Donald. He birdied the 13th to get within one of then leader Donald, but Woods played solidly and benefited from the mistakes of his closest competitors.
'I'm sure they probably hit the ball better than I did, but I made a few more putts,' said Woods.
Bernhard Langer, who led the European Ryder Cup team to victory, shot an even- par 72 and came in fifth at 11-under-par 277.
Ernie Els (71), Scott McCarron (69), Pat Perez (71), Arron Oberholser (70) and Kevin Sutherland (72) shared sixth place at 10-under-par 278.
Vijay Singh, the No. 1 player in golf, struggled to a 3-over 75 and was part of a group tied for 24th place at minus-5. Phil Mickelson, who made his season debut this week, posted a 1-under 71 and tied for 56th at even-par 288.
Daly carded a 3-over 75 in the final round and tied for 72nd at plus-6.