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."

The incident happened at a soup kitchen in Montreuil, east of Paris.
The man said he was able to dodge the axe but was stabbed in the stomach, according to a prosecutors statement.
His condition is not said to be serious. France remains under a state of emergency since last November's attacks claimed by Islamist militants.
The victim told investigators the assailants shouted "Allahu Akbar", meaning "God is greatest", and called him an "infidel dog" before running away.
He is director at Restos du Coeur, a charity which gives food packages and hot meals to the needy.
According to Reuters, the investigation is being carried out by criminal police rather than anti-terrorism units.
Since the attacks by so-called Islamic State last year, France has been on high alert.
In June, a policeman and his partner were stabbed to death outside of Paris by a man who claimed allegiance to the Islamic State.

But the objects are just some of the Mary Rose artefacts which have gone on display at Swansea University.
Researchers have been examining the artefacts from Henry VIII's warship, which was raised in 1982, to discover more about the ship's crew.
Their work has revealed that many of those who perished when the boat sank in 1545 were "superb athletes".
Sport physiologist Dr Nick Owen said the skeletons and objects raised with the Mary Rose have given them a "wealth of information".
"The abnormalities in some of the crew's radius bones shows that they'd have been supreme athletes," Dr Owen said.
"Today an Olympic bow has 48 lbs of tension, but to fire a Mary Rose bolt (arrow) would have taken well over 100 lbs."
Dr Owen believes that as well as providing a glimpse into the past, his team's discoveries can offer an insight into the injuries of modern athletes.
"You can see similar abnormalities in elite tennis and squash players," he said.
"Top sportsmen are singled out for elite training from such a young age.
"The cream of archers on the Mary Rose would have been in training since they were seven years old."
Dr Owen's team, including scientists from the University of Bradford, have already succeeded in creating an online 3D image of some of the sailors, which can be remotely studied by scientists.
The next challenge is to see what lies inside the bones.
"Once we can conduct Micro CT scans, we'll be able to see what changes being one of Henry VIII's elite archers caused internally," Dr Owen explained.
"These very fine scans will help us discover how their lifestyle and diet affected their bone structure from the inside."
The Mary Rose artefacts are on display to mark the university's research and innovation awards evening.
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.
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Police are investigating after a French charity worker said he was attacked with a knife and an axe by a couple who shouted "Allahu Akbar".
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A boot, some old skeletons and a block of wood might not sound like the type of thing to entice you to Swansea.