Never seriously threatened the rest of the way, the 20-year-old South Korean star finished with a 5-under 67 on Sunday to beat Mayu Hattori by six strokes for her second LPGA Tour title and ninth international victory of the year.
"I played for three weeks straight, so my body is naturally tired," Shin said. "This week was just really comfortable, and I felt like I could make everything. It just feels good this week. It is so nice."
The Women's British Open winner and the first player to sweep the Korea LPGA Tour's three majors in a season, Shin finished at 15-under 201 for her second victory of the year in Japan. She earned $210,000.
"Yesterday and today I was really good with my iron shots," Shin said. "Almost the best this year. It feels like I can make everything."
The event at Kinetsu Kashikojima was sanctioned by the LPGA Tour and Japan LPGA.
"I really like this tournament in Japan," Shin said. "Everyone is very friendly when I come here, so I do really want to play more tournaments in Japan."
Hattori, the Japanese player coming off a victory last week in the JLPGA's IDC Otsuka Ladies, closed with a 67. Lim Eun-a (70) was third at 8 under, and Chung Il-mi (69), Wei Yun-jye (70) and Lee Jee-young (72) followed at 7 under.
Shin played the front nine in 4 under - holing a 20-foot eagle chip on the par-5 seventh - to move four strokes ahead of Hattori and Lee. Lee birdied the 10th to cut Shin's lead to three, but had a double bogey on the par-3 11th.
"I was very nervous on the first tee," Shin said. "But I made birdies on the second and third holes and got more comfortable and confident."
Shin birdied the par-5 13th and had a six-stroke lead with four to play. She bogeyed the par-4 15th, only her second bogey on the week and first in 47 holes, then birdied the par-5 16th and closed with two pars.
Hattori had a double bogey on the par-4 12th.
"It was a tough day," Hattori said. "But this was a good experience for me. There were a lot of good players here and it's good to play against them."
She praised Shin.
"She is very consistent, having a lot of chances for birdies, never missing fairways," Hattori said. "She can easily get up and down whenever she misses greens."