Teeing off two shots off the lead in tie for third, Muto picked up two shots on the front nine and birdied five of the last nine holes in a flawless round to seal victory on 16-under 268 at Otone Country Club in Ibaraki Prefecture.
Muto, whose previous wins came at last year's Coca-Cola Tokai Classic and the 2006 Munsingwear Open KSB Cup, earned 30 million yen from the 150 million yen purse.
"I have got my form back because of the basic training I have been putting myself through," said Muto. "By starting before (Shigeki) Maruyama-san, I was not distracted by his aura and could concentrate on my play. That was one of the reasons I could win today."
South Korea's Kim Kyung Tae, who shared third-round lead with Shigeki Maruyama, carded a 69 to finish in second.
The 40-year-old Maruyama (70) fell short of capturing his first win since returning full time to the Japanese tour this season after closing another stroke back in third. He moved to the United States to play on the U.S. PGA tour in 2000.
Toru Suzuki (65), winner of last week's Mynavi ABC Championship, was a further stroke back in fourth, while Australian Wayne Perske (71) was fifth at 9-under.
The field was missing money leader Yuta Ikeda, teenage sensation Ryo Ishikawa and Shingo Katayama, who are competing in the prestigious HSBC Champions in Shanghai.