Scotland triumphed 26-13 against Japan in the first Test on Saturday, with Vern Cotter's men closing out a workmanlike victory in Toyota City.
The faultless Greig Laidlaw kicked 16 points for Scotland as Japan's lack of discipline told, with four penalties and a penalty try conceded as they made a poor start to the two-match series.
Scotland had to come from behind, however, as Japan captain Shota Horie crossed to put the hosts 7-3 up on nine minutes when Duncan Taylor missed a tackle, but away skipper Laidlaw added another two penalties to his earlier kick and converted a penalty try to give Scotland a 16-10 half-time lead.
With Japan down to 13 men - Rikiya Matsuda and Hendrik Tui sin-binned - Scotland forced their way over the line again to extend their lead shortly after the interval, prop WP Nel going over.
The impeccable Laidlaw stepped up from a wide angle to kick the conversion and extend Scotland's lead to 13 points before Yu Tamura struck with a penalty to keep Japan in the match.
Laidlaw added his fourth penalty, while a poor pass from Shokei Kin to Harumichi Tatekawa ended a fine Japan break, perhaps their best chance to score a vital try.
Tommy Seymour just failed to chase down a Laidlaw kick as the game grew increasingly stretched without any late points being scored at either end.
Japan had only beaten Scotland once in nine previous meetings since 1976 and despite late pressure in front of a partisan crowd, the Scotland defence held firm to go into next week's clash in Tokyo on a high.