Bafana Bafana goalkeepers Itumeleng Khune and Daren Keet (Photo by Lefty Shivambu/Gallo Images)
Khune has come down with a chest infection while Keet is suffering from a knee injury.
The duo have been replaced by Reyaad Pieterse of Supersport United and Wayne Sandilands of Orlando Pirates.
Bafana are set to face Cape Verde at the Estadio Nacional Stadium in Praia on Friday, September 1.
The teams will then meet in the return leg at the Moses Mabhida Stadium in Durban four days later.
