Jack Cornelsen replaces Ben Gunter on the flank while Keijiro Tamefusa comes in for Shuhei Takeuchi in the front row from the team that started last Saturday's 41-10 defeat by Ireland.
Gunter is unavailable because of personal reasons while Takeuchi drops to the bench.
Veteran loose forward Michael Leitch and back Tiernan Costley are both out with injury, officials added.
Japan lost at home to Australia last month before embarking on their European tour, where they have lost to South Africa in London and to Ireland over the last fortnight.
They have a last test on tour in Georgia on November 22.
Japan team to face Wales:
Starters: 15-Yoshitaka Yazaki, 14-Kippei Ishida, 13-Dylan Riley, 12-Charlie Lawrence, 11-Tomoki Osada, 10-Lee Seung-sin, 9-Naoto Saito, 8-Faulua Makisi, 7-Kanji Shimokawa, 6-Jack Cornelsen, 5-Warner Dearns (captain), 4-Epineri Uluiviti, 3-Keijiro Tamefusa, 2-Kenji Sato, 1-Kenta Kobayashi
Replacements: 16-Shodai Hirao, 17-Sho Furuhata, 18-Shuhei Takeuchi, 19-Harry Hockings, 20-Tyler Paul, 21-Kenta Fukuda, 22-Shinya Komura, 23-Kazuma Ueda.