Wataru Ikeda replaces Kiyonori Tanaka at scrum-half and Hayato Daimon displaces Hiroki Mizuno on the wing.
Yukio Motoki will play his fifth game against Wales, winning his 71st cap at centre in place of Seiichi Shimomura.
Ikeda, Damon and Motoki all started in the 100-8 defeat by Scotland two weeks ago.
Apart from Motoki, the most-capped player is flanker Naoya Okubo with just 22 caps, the inexperienced side led by No 8 Takuro Miuchi.
Japan: R Miki; K Kubota, M Mukoyama, Y Motoki, H Daimon; H Yoshida, W Ikeda; Masahito Yamamoto, T Yamaoka, R Yamamura, H Kiso, T Kumagae, F Mau, N Okubo, T Miuchi (capt).
Replacements: Mitsuga Yamamoto, T Nishiura, K Kubo, T Yamaguchi, K Tanaka, S Imari, T Otao.