Tokyo - Greig Laidlaw has been replaced as scrumhalf, captain and goalkicker by Henry Pyrgos among six changes in a Scotland side that was tired and sore after beating Japan in the first Test last weekend.
Meanwhile, Japan changed only two - both outside backs - for the second Test on Saturday in Tokyo, after losing the first 26-13.
Laidlaw was dropped to the reserves to give regular back-up Pyrgos a go.
Rory Sutherland received his first start, and staying at loosehead prop, where he replaced the injured Alasdair Dickinson after three minutes last Saturday.
Tighthead prop Moray Low was also in for the injured WP Nel, and Josh Strauss in on the blindside flank.
Centre Peter Horne and wing Sean Maitland were promoted from the reserves to starting roles.
"It was a very tiring game, and we expect something similar this weekend," Scotland coach Vern Cotter said.
Scotland dominated possession, but put a healthy gap on the scoreboard only after Japan was reduced to 13 men on yellow cards just before half-time.
Riyika Matsuda, one of those sin-binned, will start at fullback for his third cap, while veteran Male Sa'u was back on the right wing. Another Rugby World Cup player, No 8 Ryu Koliniasi Holani, was summoned to the reserves.
15 Riyika Matsuda, 14 Male Sau, 13 Tim Bennetts, 12 Harumichi Tatekawa, 11 Yasutaka Sasakura, 10 Yu Tamura, 9 Kaito Shigeno, 8 Amanaki Mafi, 7 Shokei Kin, 6 Hendrik Tui, 5 Naohiro Kotaki, 4 Hitoshi Ono, 3 Kensuke Hatakeyama, 2 Shota Horie (captain), 1 Keita Inagaki
Substitutes: 16 Takeshi Kizu, 17 Masataka Mikami, 18 Shinnosuke Kakinaga, 19 Kotaro Yatabe, 20 Ryu Koliniasi Holani, 21 Keisuke Uchida, 22 Kosei Ono, 23 Mifiposeti Paea
15 Stuart Hogg, 14 Tommy Seymour, 13 Matt Scott, 12 Peter Horne, 11 Sean Maitland, 10 Ruaridh Jackson, 9 Henry Pyrgos (captain), 8 Ryan Wilson, 7 John Barclay, 6 Josh Strauss, 5 Jonny Gray, 4 Richie Gray, 3 Moray Low, 2 Stuart McInally, 1 Rory Sutherland
Substitutes: 16 Fraser Brown, 17 Gordon Reid, 18 WP Nel, 19 Tim Swinson, 20 John Hardie, 21 Greig Laidlaw, 22 Huw Jones, 23 Sean Lamont