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.
13. Chris Harris
Big hitting tackle after quarter hour had crowd wincing but strong first half barely faded in the second of a big game for the Scottish centre. 7 Photo: ANDY BUCHANAN
14. Darcy Graham
Headlines will be about Hogg but Graham threatened to steal the limelight with a strong wide display before being replaced by Blair Kinghorn. 8 Photo: ANDY BUCHANAN
15. Stuart Hogg (C)
History-maker started like a coiled spring and upon release bounded forward to start and finish the move for his record-setting try. Scotland wouldn't relinquish the lead. 8 Photo: ANDY BUCHANAN
16. Substitutes
Dylan Richardson (pictured) made a late introduction after Javan Sebastian's debut off the bench. Pierre Schoemann made a big impression and Stuart McInally scored within seconds of entering the field. Photo: ANDY BUCHANAN