Ireland's Darren Clarke fired a level-par 71 to finish tied for third with Justin Rose, two strokes behind Japan's Kaname Yokoo, who shot a two under 69 to clinch the Dunlop Phoenix event at the Phoenix Country Club at Mizayaki
In winning Asia's richest tournament Yokoo picks up a 40 million yen winner's cheque.
Fast-finishing Spaniard Sergio Garcia had four birdies in the last six holes to card a five-under par 66 to take second, one stroke ahead of South Korean K.J. Choi who posted the lowest round of the day, a seven-under-par 64.
Huge galleries did their best to inspire Tiger Woods to a trademark final-day charge, but the world number one again missed key putts on the slick greens to close with a four-under-par 67. The result meant that Tiger finished eighth at nine under par.
Yokoo said he was delighted to finish ahead of the world number one for the first time.
"I'm really happy to win today against such a good field," said Yokoo, who has endured a miserable year with the putter to slump to 130th on the US PGA tour.
"I figured Tiger would make a run but after I made four birdies in a row, I was eight strokes ahead and I felt pretty good but you never know with Tiger."
Despite stumbling late in his round with two bogeys in the last five holes, including the par-five final hole where he three-putted after finding a fairway bunker off the tee, Yokoo held on to break a winless streak dating back to the Japanese Matchplay championship in 2000.
"It wasn't the way I wanted to finish but thankfully nobody eagled the final hole to force a playoff," said a relieved Yokoo.
Garcia had opened shakily with a bogey on the third hole but hit back with birdies on the par-five fourth and seventh holes and added another on the eighth hole after a glorious short-iron approach.
A costly bogey on 10 appeared to have ended his challenge but the young Spaniard rallied courageously with birdies on the 13th, 15th, 16th and the final hole in a thrilling finale.
"Not in second place again!" said Garcia, who lost a playoff in 1999 to Denmark's Thomas Bjorn.
"I wanted to win so bad this year. I could have done better today since I missed several short birdie putts on the front nine. My shots were good and the course was terrific. I'll come back again and try to win this tournament," he added.
Woods tried in a vain to launch a challenge but although he putted better than the previous two days, several short misses proved decisive.
"I played really well the last three days but I didn't putt well until today," he said.