Philander, the number two ranked bowler behind teammate Dale Steyn in Tests, woke up with a stiff lower back and was replaced by Rory Kleinveldt.
Kleinveldt initially missed out on selection when legspinner Imran Tahir was preferred in the Proteas bowling attack after the drawn Brisbane series opener.
"Vernon woke up complaining about lower back stiffness, he progressively got worse and didn't respond to the treatment from our physiotherapist," team manager Mohammed Moosajee said.
"He will go for an MRI scan as soon as possible to give us a clearer indication of the symptom."
Australia won the toss and chose to bat in ideal conditions at the Adelaide Oval.
Vernon Philander ruled out of second Test against Australia with a back injury
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