Greig Laidlaw was replaced as halfback, captain and goalkicker by Henry Pyrgos among six changes by a Scotland side that was tired and sore after beating Japan last weekend in the first rugby Test.
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 bench 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 last Saturday after three minutes. Tighthead prop Moray Low was also in for the injured WP Nel, and Josh Strauss in on the blindside flank.
Centre Peter Horne and winger Sean Maitland, the British Lion, 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 were reduced to 13 men on yellow cards just before halftime.
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.
Japan: Riyika Matsuda, Male Sau, Tim Bennetts, Harumichi Tatekawa, Yasutaka Sasakura, Yu Tamura, Kaito Shigeno; Amanaki Mafi, Shokei Kin, Hendrik Tui, Naohiro Kotaki, Hitoshi Ono, Kensuke Hatakeyama, Shota Horie (capt), Keita Inagaki. Res: Takeshi Kizu, Masataka Mikami, Shinnosuke Kakinaga, Kotaro Yatabe, Ryu Koliniasi Holani, Keisuke Uchida, Kosei Ono, Mifiposeti Paea.
Scotland: Stuart Hogg, Tommy Seymour, Matt Scott, Peter Horne, Sean Maitland, Ruaridh Jackson, Henry Pyrgos (capt); Ryan Wilson, John Barclay, Josh Strauss, Jonny Gray, Richie Gray, Moray Low, Stuart McInally, Rory Sutherland. Res: Fraser Brown, Gordon Reid, WP Nel, Tim Swinson, John Hardie, Greig Laidlaw, Huw Jones, Sean Lamont.
