Scottish halfback Ali Price has been ruled out of the tournament after suffering a foot and ankle knock in Sunday's 3-27 loss to Ireland. He is being replaced by Edinburgh halfback Henry Pyrgos. He has 27 caps to his credit, the last being against Australia in 2017.
Earlier, flanker Hamish Watson was forced out of the remainder of the World Cup when suffering a serious knee injury against Ireland.
Scotland face a crucial pool game when playing Samoa on Monday in Kobe.
Coach Gregor Townsend said: "We're disappointed for Ali to have to return home so early in the tournament.
"Both Ali and Hamish had invested a lot of effort into being in their best physical shape for the World Cup and it's a shame that they've only been involved in one game.
"However, we have a lot of belief in our wider group and the two new players, Magnus Bradbury and Henry Pyrgos, who have been given this opportunity," he said.
For Samoa, who beat Russia 34-9 on Wednesday even after playing with two men in the sin-bin at one stage, there was the likely loss of No.8 Afaesetiti Amosa who was taken from the field with a serious knee injury after scoring his side's second try.
Coach Steve Jackson said Amosa had been taken for a scan after the game but the injury did not look good.
Hooker Motu Matu'u, who was one of the sin-bin offenders for a high tackler, hit his head in the incident and failed an HIA and did not return at the end of his suspension.
Halfback Dwayne Polataivao did not come out after time and he also failed an HIA.
Japan are the other team in Pool A who they All Blacks could potentially face in a quarterfinal. The Brave Blossoms came through largely unscathed from their opening bonus point win over Russia.