The 30-year-old had to be helped off the field after an accident during a training session for the second Test against India in Bangalore.
Scans revealed a ligament tear in his left ankle, with Philander due to be out for "at least six to eight weeks".
England's Test series against South Africa starts in Durban on Boxing Day.
"Vernon stepped on Dean Elgar's foot by accident in our warm-up," said Proteas batsman AB de Villiers. "It was a very freakish accident, to be honest. He is very unlucky."
South Africa have called up paceman Kyle Abbott to replace Philander, who has taken 126 wickets in 32 Tests, for the rest of the four-match series, with the visitors currently trailing 1-0.
Philander's injury could mean he misses the first two Tests of England's four-game series in South Africa - the second Test in Cape Town on 2 January quickly following the first.
"The first Test match against England is six weeks away so it will be a tight schedule to get him ready and rehabilitated to make that Test match," said South Africa team manager Dr Mohammed Moosajee.
"Once he has been assessed back home in Cape Town and a proper programme for physio and rehabilitation has been put into place we will have a clearer understanding."
South Africa bowler Vernon Philander could miss the start of next month's Test series with England after injuring his ankle in a warm-up football game.