"It's a huge loss for the team," said coach Jake White, who has yet to name a replacement.
"He is such a great player who would have played a huge role in our campaign in France. It would have been fascinating to see him in action with the likes of Schalk Burger at the World Cup."
Spies was looking at the bright side, saying: "It would have been great to be in France, but I must accept that it is good that they diagnosed the problem much earlier.
"Matters could have been worse had I continued playing. I wish the team all the best in France, and am also looking forward to playing for the Springboks again in the near future."