Padraig Harrington, who won here in 2002, bogeyed 16 and 18 to finish two shots back at 14-under-par 270.
Colin Montgomerie (71), who had least a share of the lead after each of the first threes rounds, and Jay Haas (69) shared third place at minus-13. Miguel Angel Jimenez took fifth place at 11-under-par 273 after final-round 70.
With the win, Woods joined Davis Love III (2000 and 2003) as the only two-time winners of this event. Woods also owns three runner-up finishes in the six years of the tournament.
Woods, as he normally does here, donated his first-place check of $1,250,000 to the Tiger Woods Foundation, which is run by his father and hosted this event.
'It is pretty cool,' said Woods of having his father following his play. 'Obviously to have my dad around, as focused and driven as he is with the foundation, it's exciting. And to have him out there makes it even more special. I think it was two days ago, it's the first time I've seen him on the golf course following my play in a lot of years.'
Woods wasted no time in erasing the two-stroke deficit he was in to start the round. He drained a birdie at the first and came right back with an up-and-down birdie on No. 2 to take the lead as Montgomerie bogeyed the first.
Montgomerie tied Woods in the lead with a birdie at the third. That proved to be the Scotsman's last piece of the lead as he bogeyed the next to drop back to 12 under.
Woods two-putted for birdie at the par-5 fifth to move to 14 under. Harrington birdied the sixth to closed within one shot, while Monty tried to remain close with a chip-in birdie also on No. 6 at Sherwood Country Club.
Harrington kept charging and joined Woods in the lead as he birdied the eighth from 9 feet out. Woods parred the final four holes of the front side to make the turn tied at minus-14 with Harrington.
'I felt like I needed to shoot 3 or 4 under par on that front side,' said Woods, who shot 3-under 33 on the front nine. 'I figured the guys were going to go low. I figured Monty or Jay behind us was going to put something up on the front side. I didn't think Harrington was going to shoot 5 under par on the front nine. So I had to keep pace.'
Woods nearly holed his second shot to the par-4 10th from 59 yards away. His ball danced around the right edge and came to rest within a foot of the cup and he kicked in the birdie to move to 15 under.
Harrington, playing one group ahead of Woods, two-putted for birdie at the par-5 13th to tie for the lead. Woods, however, also two-putted for birdie to retake a one-shot lead.
Both players parred 14 and 15, before the big turning point at 16. Harrington lost his second shot to the par-5 16th well right of the green. It came to rest in a hazard.
The Irishman played it from there, but blasted it over the green and into a bush. Harrington then hit his fourth shot from the bush left handed. He managed to get his ball out of the bush before getting up and down for bogey to slip to minus-14, two strokes behind Woods.
Woods also struggled on the 16th, but it was not all his fault. He left his second shot short and under a tree. Woods pitched his third short of the green. As Woods hit his pitch shot, his fourth stroke, a fan yelled disrupting Woods' swing.
Woods regained his composure and rolled in the 6-foot, par-saving putt. Harrington moved back within one shot of Woods with a 4-foot birdie putt at 17. Woods two-putted for par on the par-3.
Harrington pulled his drive left off the 18th tee. With a tough lie, he decided to lay up. Harrington's strategy back-fired when his third shot missed the green right. He did get up and down for bogey to close at minus-14.
'I had 5-wood in to 16, like I did in 2002,' Harrington said. 'Two years ago I hit it right in the middle of the green when I wasn't feeling too good. This year, I hit it right when I was feeling great. These things happen in golf. Sometimes they come off, sometimes they don't.'
Woods hit the fairway at the last before dropping his second shot 18 feet from the cup. He calmly two-putted for par and the two-stroke win.
'I feel very comfortable with my swing,' said Woods, who went through a swing change this past season. 'It was exciting coming down the stretch there and holding up. Every shot I wanted to hit, I hit. I just didn't make any putts today.'
Jim Furyk, who played with Woods, closed with a 3-over 74 to take sixth place at 8-under-par 276. Stewart Cink was one stroke further back at minus-6 after a closing 70.
World No. 1 Vijay Singh rallied with a 3-under 68 Sunday to tie Fred Couples for eighth place at 5-under-par 279. Chad Campbell ended at minus-4 after struggling to a final-round 73.
Chris DiMarco (3-under-par 281), John Daly (minus-2) and 2003 champion Davis Love III (minus-2) were the final players in red figures in the 16-player field.
Kenny Perry took 14th place at even-par 284 after closing with his second straight 69. Stephen Ames (72) and British Open champion Todd Hamilton (73) finished in last place at 5-over-par 289.