He is now set to return home on Monday, although England head coach Brian Ashton has not yet made a decision on any possible replacement.
Noon's Newcastle colleague Toby Flood would be the favourite to replace him as England head into a critical Pool A appointment with Samoa in Nantes next Saturday.
Noon's injury has been diagnosed as a grade two strain to a ligament in his left knee, which was confirmed following a hospital scan.
England team doctor Simon Kemp said: "Jamie will not be able to take any further part in the tournament.
"Arrangements are in place for him to return to Newcastle for ongoing rehabilitation, and it is likely he will return on Monday."
Realistically, Noon can expect a six week lay-off with this type of injury.
England though, have received better news surrounding full-back Jason Robinson, who limped off during the Springboks clash with a hamstring injury.
It was initially feared that Robinson would miss the rest of the competition, but England are optimistic he will be able to play a further part.
Robinson has suffered a strain to his left hamstring, but he will remain with the squad, undergoing further treatment with a chance he could be involved in future games.
England are also keeping a close eye on fly-halves Jonny Wilkinson (ankle ligament sprain) and Olly Barkley (hip), who were both unfit to face South Africa.
Their combined absence meant a first England start in the number 10 shirt since 1999 for Mike Catt.