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.
. Japan's flanker Pieter Labuschagne (C) is tackled during the Autumn International friendly rugby union match between Scotland and Japan at Murrayfield Stadium in Edinburgh on November 20, 2021. (Photo by ANDY BUCHANAN / AFP) (Photo by ANDY BUCHANAN/AFP via Getty Images)
Japan's flanker Pieter Labuschagne (C) is tackled during the Autumn International friendly rugby union match between Scotland and Japan at Murrayfield Stadium in Edinburgh on November 20, 2021. (Photo by ANDY BUCHANAN/AFP via Getty Images) Photo: ANDY BUCHANAN
. Jamie Bhatti
Yellow-carded early in the second half cost Scotland their cushion and replaced by Watson. 5 Photo: Ross Parker - SNS Group
. 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
. Zander Fagerson
Stood up strong to everything asked of him over the afternoon. 6 Photo: Craig Williamson - SNS Group / SRU
. 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
. Grant Gilchrist
Dominated line-out early on and notable when he didn’t, because it cost Scotland. Important. 7 Photo: Ian MacNicol
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