London Irish flanker Blair Cowan has replaced GUINNESS PRO12 star Gilchrist in the squad.
Posting on his Twitter profile, Gilchrist said: "Devastated. Big thanks for the support. All the best to the boys for the rest of the tournament."
Gilchrist has endured a tough year after suffering a broken arm in October, which then required a second operation in February.
It meant he only made three GUINNESS PRO12 appearances last season and faced a race against time to make the World Cup.
Vern Cotter's side face South Africa on Saturday as the top two in Pool B meet at Newcastle United FC's St James' Park.
"He's pretty gutted," Scotland's assistant coach Duncan Hodge said.
"Obviously, the World Cup is the pinnacle of anyone's career but you look back on the year he's had and he's worked so hard as well to get fit.
"When we started off in June he was 12 months behind everyone else in terms of work, so for him to get where he got to, and playing as well, was an achievement in itself and to get shot down like that... well, we all feel for him.
"However, you just need to look around. England, Wales, everyone is picking up injuries, and it's just the nature of the game. It's unfortunate."
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Guinness PRO12 Edinburgh News
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