The recurrence of the injury which almost sidelined him from the first Test in Cape Town - in which he earned his fourth man of the match award - means he will not play in the second and final match of the Test series.
"Vernon's hamstring strain will require a seven to 10 day recovery period at the very least," Proteas team manager, Mohammed Moosajee, said in a statement.
"Although he is responding to treatment received over the past few days, we feel it's unlikely that he'll recover in time for this week's Test. Besides, with the Pakistan series less than a month away, it's not worth the risk of aggravating the injury."
Cape Cobras team-mate, Rory Kleinveldt, will earn his third Test cap as Philander's replacement. All rounder Ryan McLaren has been added to the squad as cover.