Gregor Townsend’s side took an early lead through Duhan van der Merwe before a historic try for Stuart Hogg restored Scotland’s lead.
The score etched the captain’s name in the record books as the all-time record scorer with 25 international tries.
Darcy Graham extended Scotland’s lead before the interval and though Japan took advantage of Jamie Bhatti’s yellow-card, Scotland maintained their lead and saw out the match to end the series with a win.
Here’s how the players rated at BT Murrayfield.
1. Jamie Bhatti
Yellow-carded early in the second half cost Scotland their cushion and replaced by Watson. 5 Photo: Ross Parker - SNS Group
2. George Turner
Returning from injury and no sign of hangover with series of string stops in the second half with Scotland depleted. 6 Photo: Craig Williamson - SNS Group / SRU
3. Zander Fagerson
Stood up strong to everything asked of him over the afternoon. 6 Photo: Craig Williamson - SNS Group / SRU
4. Scott Cummings
Plundered forward in the second half and earned a break for the last ten minutes after a powerful shift. 6 Photo: Craig Williamson - SNS Group