Fifa has ordered Everton to release Steven Pienaar for international duty ending his chances of playing in Tuesday's Carling Cup semi-final.
South Africa were expecting Pienaar to leave Everton on Sunday
South African Pienaar was due to play against Chelsea before flying to compete in the African Cup of Nations.
Everton boss David Moyes thought Pienaar would arrive 14 days before South Africa's first match, complying with Fifa regulations.
But Fifa said the ruling applies to the start of the tournament on 20 January.
South Africa's first match is not until January 23 against Angola and Moyes had hoped Pienaar could join fly out to Pretoria on Wednesday.
An Everton spokesman said: "Steven will be going to London today, but not to Stamford Bridge. He will be flying out from Heathrow.
"We have been contacted by Fifa and told he has to be released by us ahead of the Chelsea match."
Pienaar trained with Everton on Monday but by mid-afternoon, South Africa had formally asked Fifa to intervene to end the confusion.
Moyes' stance was almost certainly prompted by having Nigerian internationals Ayegbeni Yakubu and Joseph Yobo available for the tie at Stamford Bridge.
The pair will play for Everton before being released to join their country's training camp in