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.
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.