The 19-year-old Japanese student – who has won back-to-back Asian Amateur titles and made international headlines with his performance at Augusta National in April – eagled the last hole to win by two strokes and become only the third amateur to win on the Japan Golf Tour.
It caps a remarkable year that has included finishing low amateur and T-27 at the Masters. He then secured a return to Augusta and a spot in International Final Qualifying (IFQ) for The Open 2012 with the successful defence of his Asian Amateur title at The Singapore Island Country Club (SICC) last month.
The win also means that Matsuyama can expect to improve on his sixth place when the World Amateur Golf Ranking (WAGR) is announced on Wednesday.
The tournament, which was reduced to 54-holes due to weather delays on Friday, saw the Tohoku Fukushi University student begin the final day two shots behind overnight leader Toru Suzuki before signing for a four-under 68 and a 13-under 203 total.
Speaking after his victory, Matsuyama said: "I didn't expect to win this tournament. I wanted to be just the low amateur here, but to my surprise, I won. The experience of playing at the Masters - the biggest stage of all in golf - has helped me play as usual even in an intense final round like today's."
He overcame one of the strongest fields of the year on the Japan Golf Tour to secure the win. South African Schwartzel closed with a 69 to share third, while Japan’s Ryo Ishikawa - the defending champion - recorded his second career hole-in-one at the 17th for a round of 67 and a tie for eighth.
Matsuyama has previously stated that he will remain amateur and complete his final two years of college. He is expected to be in the field when the fourth Asian Amateur Championship is staged at Amata Spring Country Club in Chonburi, southeast of Thailand’s capital city of Bangkok, from November 1-4, next year.