Both players have a mild infection.
Bjorn Fortuin, Rilee Rossouw and Tristan Stubbs have been added to the squad.
South Africa are 1-0 up in the three-match series after winning the opening ODI by nine runs.
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PROTEAS
Proteas
Bavuma, Shamsi to miss second ODI
Proteas captain Temba Bavuma and spinner Tabraiz Shamsi have been ruled out of the second ODI against India in Ranchi.
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