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The Sunderland captain was reinstated into the Switzerland squad by manager Murat Yakin along with striker Breel Embolo after a scandal emerged last month.
The World Cup quarter finalists dumped both of the players from the previous four games in the competition following an investigation into them obtaining fake Covic certificates.
Xhaka and Embolo were fined £136,000, suspended for two years on condition that the players do not commit any further violations.
They were both invited back, but former 34-year-old Arsenal ace Xhaka won't be able to add to his 152 caps when he faces the Scots.
A Swiss FA statement confirmed: "Granit Xhaka has withdrawn from the Swiss national team camp due to a calf injury."
Switzerland need just a point on Friday against Slovenia to win the group.