Vern Cotter's men, unable to score a try on a hot and humid evening at the Ajinomoto Stadium, gained all their points through penalties, with scrumhalf Henry Pyrgos converting three and his replacement Greig Laidlaw slotting four.
The Brave Blossoms, looking to avenge their loss to the visitors a week ago, scored a scintillating early try through scrumhalf Kaito Shigeno, who ran through the length of the pitch.
Yu Tamura converted and kicked three penalties for the hosts.
The crowd of 34,000, including the emperor and empress of Japan, was entertained by bruising runs from Japan number eight Amanaki Mafi, who again proved a handful for the visitors after giving Scotland a scare during last year's World Cup.
Japan, who led 16-9 at halftime, let themselves down through indiscipline just as they did in the first game in Toyota city.
Laidlaw proved to be the difference by punishing the hosts each time Scotland made forays into the Japanese half.
The Brave Blossoms put Scotland under siege in the second half but were again left to rue disciplinary lapses, which Laidlaw took full advantage of.
Scotland made six changes to the team from the first test with Pyrgos handed the captaincy.
Japan made only two changes, with Male Sau coming in the wing and Rikiya Matsuda, who was sin-binned during the first test, chosen as fullback.
(Editing by Ed Osmond)
