Kim's third round of 75 appeared to have left him too far off the third round lead to have had any chance, especially given that lead was held by the very much in form Matsuyama.
Kim, playing one hour ahead of Matsuyama, raced through the opening nine in 29 and by the time Matsuyama reached the 10th tee he trailed Kim by one shot. One hole later Kim's lead had stretched to two over Matsuyama, Fujimoto and Fujita.
Kim would go on to record a round of 65, the best of the day by three shots and none of the 18 players still on the golf course when he finished his round could catch him.
Fujimoto recorded the second best round of the day to move from a share of 5th to equal second.
Almost inexplicably, Matsuyama stumbled to a final round of 75 which included five bogeys in his first seven holes but even then he had a chance to force a playoff with a par at the last. Unfortunately be bogeyed and fell back into a share of second.
Kim's only other victory in Japan has come at the Vana H Cup KBC Augusta event in Fukuoka last August although he was also three times runner-up in 2012.
Scott Strange, Brendan Jones and Paul Sheehan finished as the leading Australasians in 15th position, Richard Tate was 31st, David Smail was 39th, Brad Kennedy 45th and Steve Conran 55th.
Matsuyama leads the Japan Tour money list with nearly $A500,000 courtesy of his victory at the Tsuruya Open, two runner-up finishes and a 10th place in the season opening Token Homemate Open.
Strange leads the Australians on the money list this season although he does not official status on the Tour. He is in 11th position, while Brendan Jones is 16th.