Shin had six birdies in a bogey-free round at the Kintetsu Kashikojima Country Club for a 36-hole total of 13-under 131 .
Shin, who is No. 1 in the LPGA rankings, won here in 2008 and put herself in position to win her second tournament of the year.
“This is a course where you can get some good scores so my plan is to be aggressive tomorrow,” Shin said. “I’m satisfied with the way I’m playing even though I didn’t feel that good physically.”
Lewis had the day’s lowest round of 64 to finish two strokes back at 11 under.
Taiwan’s Yani Tseng shot a 65 and was tied for third with Japan’s Miki Saiki (67).
“My round was very good today,” Lewis said. “I could have done a bit better on the front nine, but all in all I was satisfied with my score.”
Shin, who held an overnight share of the lead with Japan’s Yukari Baba, took the lead with a birdie on the par-5 16th hole and added another on the par-4 18th.
Lewis birdied four of the last six holes and looked set to take the lead before Shin’s strong finish.
American Morgan Pressel shot a 69 for fifth at 8-under 136 in the $1.2 million tournament.
Japanese star Ai Miyazato struggled with her game for the second day in a row with a 79 that knocked her out of contention. Miyazato, who has five wins this season, came into the tournament vying to become the first player from Japan to capture Player of the Year honors since Ayako Okamoto in 1987. She is second in the race, two points behind Tseng.