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.
9. Ali Price
Found his range after a loose start but picked up. Eventually replaced by George Horne. 5 Photo: Craig Williamson - SNS Group / SRU
10. Finn Russell
Hit post with first conversion attempt but kicking otherwise on point and kept Scotland ticking. 8 Photo: Ross Parker - SNS Group / SRU
11. Duhan van der Merwe
Scored the first try and palpable excitement with every possession among the crowd. 7 Photo: Ross Parker - SNS Group / SRU
12. Sam Johnson
Clever grubber kick after 19minutes almost sent Harris through. Otherwise solid with strong territory in the second half. 7 Photo: Craig Williamson - SNS Group / SRU