Gcaba, who plays his club football for Orlando Pirates, was added to Shakes Mashaba's squad on Monday two days after they were forced to send Phungwayo home.
The 27-year-old failed to recover in time from the medial collateral ligament damage he suffered to his left knee earlier this month, and he was removed from the squad on Saturday.
Mashaba is unlikely to start Gcaba during the competition in Equatorial Guinea, but he will be needed should centre backs Eric Mathoho, Rivaldo Coetzee and Thulani Hlatshwayo suffer any injuries.
Having made his international debut in 2012 the 28-year-old has not featured since for South Africa, and will be hoping to impress at the tournament to cement a long-term place in Mashaba's squad.
South Africa begin their AFCON campaign against Group C rivals Algeria in Mongomo on January 19, before matches with Ghana and Senegal.
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