John only joined the U21s ahead of last Saturday's pool match against England after providing injury cover for the senior Scotland squad in South Africa. He hyper extended his elbow joint in a tackle at the very end of the game, which the Scots lost 31-12.
Centre Garry Law is also ruled out with an ankle injury he sustained in the opening pool game with Australia.
Scotland U21 coach Iain Paxton said: "It's frustrating as we'd expected John to make a big contribution to our championship. After being without him for the first part of the tournament, he came in and played really well and so we're disappointed to lose him with two games still to play.
Flying out to replace John and Garry tomorrow are Calum Forrester and Andrew Easson, who were both part of the Scotland squad for the IRB World Series Sevens tournaments in Paris at the end of May and London earlier this month.
Callum of GHA is a member of the Glasgow Warriors Academy and the West Of Scotland Institute of Sport.