The 15-time major winner Woods finished 19-under par to equal US legend Sam Snead's all-time record of 82 US PGA Tour victories set 54 years ago.
Woods, in his first outing since arthroscopic knee surgery two months ago, broke into a huge smile after he safely got up and down from a greenside bunker at the 18th for a birdie and three-under final round of 67.
The inaugural US PGA Tour event in Japan had seen Friday's play washed out by the fringes of a typhoon that dumped almost 10 inches of rain on the course 50 miles (80km) from Tokyo, forcing play into an extra day.
World number two Rory McIlroy finished birdie-birdie for a 67 and a share of third place on 13-under par with South Korea's PGA Tour Rookie of the Year Im Sung-jae who carded a fine five-under 65.
Woods resumed his final round, suspended due to darkness on Sunday, at 7.30am on the long par-12th at Accordia Golf Narashino Country Club but saw his overnight three-shot cushion over Hideki Matsuyama immediately cut to two.
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The 15-time major winner missed the green with his approach and fell back to 17-under par.
The damage could have been worse, but Matsuyama underhit his 20-foot birdie putt on the short 13th and remained at 15-under.
Woods's early-morning putter was cold, and on the short 13th he failed to take advantage of a precision tee shot to six feet.
Up ahead on the 14th green, Matsuyama inexplicably spurned a golden opportunity to reduce the deficit to one as he missed a four-foot birdie putt after a wonderful pitch shot.
Woods was faced with a similar line of putt as Matsuyama on 14, but from 20 feet further away. He did not miss, and restored his three-shot advantage with four holes remaining.
Woods missed another birdie chance, from 10 feet, at the 15th and was watching from the 16th tee 181 yards away as Matsuyama walked in a 20-footer for his first birdie of the day to get to 16-under.
Woods found the green safely but his putt from 25 feet never threatened the hole leaving him two ahead with two to play.
Matsuyama crushed a drive down the middle of the 491-yard 17th and found the putting surface with his approach.
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Woods, a group behind, followed with a smooth drive into the heart of the fairway.
Matsuyama's fine attempt to hole the putt slid by on the left and he stayed two adrift with only the par-five 18th to rescue his challenge.
Woods found the heart of the green with his approach to 17 and two-putted safely for par.
Matsuyama found the sand twice on the 18th.
Needing to get up and down to have any chance, Matsuyama's bunker shot flew to the back of the putting surface and his brave challenge was over as he finished 16-under with a final round 67.
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