The slightly-built Korean, who has not missed a single cut in Japan this season, overcame the tough playing conditions with four birdies against one bogey for a seven-under 206 at the Ibaraki Country Club.
All six Indians had missed the cut at the halfway stage on Friday.
Asian Tour honorary member and Asia's first male Major champion Y E Yang of Korea sank a 15-footer eagle putt on the last for a 69 to share second place with Japan's Tetsuji Hiratsuka (71), Masahiro Kawamura (71) and Akio Sadakata (68).
