Philander hobbled off the field after sending down just four overs in Sunday's 130-run loss to India in Melbourne. When he batted, he was dismissed for nought.
"Vernon sustained a Grade 1 hamstring strain which was confirmed by the scans done in Sydney on Monday afternoon," Proteas team manager Mohammed Moosajee said Tuesday.
"The recovery period for a hamstring strain normally takes a week to 10 days which makes him unavailable for the match against the West Indies in Sydney on Friday."
"The Ireland match, as we speak, is eight days away," he said. "With the recovery period being a week to 10 days, we have to give him every opportunity to make sure that he can be available.
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"At the same time we don't want to be foolish by taking short-cuts, we will go through the usual treatment protocols and the return-to-play protocols.
Philander, who took two for 30 in South Africa's opening 62-run win over Zimbabwe, has taken 37 wickets in 26 ODIs.