Gregor Townsend has made seven changes to the starting XV from the side which lost 30-15 to South Africa in Edinburgh last weekend.
The head coach has brought back Darcy Graham and Sam Johnson to the backline in place of Rufus McLean and Matt Scott, respectively.
There are five changes in the pack. Glasgow Warriors prop Jamie Bhatti earns his first Scotland start since August 2019 as he replaces Pierre Schoeman at loosehead.
Bhatti is joined in the front row by club-mate George Turner who has recovered from a rib injury sustained against Australia and starts ahead of Stuart McInally.
Glasgow lock Scott Cummings makes his first Scotland appearance of the season as he completes his return from a hand injury to partner Grant Gilchrist in the second row.
Josh Bayliss makes his first start for Scotland at No 8 after his debut off the bench against Australia two weeks ago.
Edinburgh flanker Hamish Watson returns to the starting XV at openside after being on the bench against the Springboks, with Jamie Ritchie returning to the blindside.
There is the possibility of two Scotland debuts from the bench, with Scarlets prop Javan Sebastian and Cell C Sharks back-row forward Dylan Richardson named among the replacements.
Townsend said: “We have had a positive week as a squad and want to close out our Autumn Nations Series campaign with an improved performance against a Japan side we expect to challenge us from the outset on Saturday."