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.
"It's just crazy. It's a lot," the 43-year-old Woods said of his 82nd official Tour victory. His first came 23 years ago this month in Las Vegas when he was just 20.
|Tiger Woods (AP-Yonhap)|
"It's been a long week, five days at the top of the board is a long time. It was definitely stressful."
Woods led from gun to tape in the inaugural US PGA Tour event in Japan, which saw 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 7.30 am on the long par-12th at Accordia Golf Narashino Country Club but saw his overnight three-shot cushion over Matsuyama immediately cut to two.
The 15-time major winner missed the green with his approach and fell back to 17-under par as he failed to get up and down.
Woods's early-morning putter was cold, and on the short 13th he failed to take advantage from six feet for a birdie.
Up ahead on the 14th green, Matsuyama inexplicably spurned an easy opportunity to reduce the deficit to one as he missed a four-foot birdie putt.
Woods was then 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.
Matsuyama crushed a drive down the middle of the 491-yard 17th and found the putting surface with his approach.
Matsuyama's fine attempt to hole the putt slid by on the left and he found sand twice on the par-five 18th as he went in search of an eagle.
Matsuyama's greenside bunker shot flew the flag and when he missed the long putt back his brave challenge ended at 16-under for the tournament after a final-round 67.
"This was big," said a smiling Woods.
"Hideki made it tight. It was a lot closer than what people probably thought. Hideki put heat on me." (AFP)