Cape Town - Sibusiso Khumalo and Puleng Tlolane were missing from Tuesday morning's training season, according to the Bafana Bafana Twitter account.
Khumalo has flu while Tlolane is "sorting out passport ahead of travel to Lesotho".
Earlier, Daniel Cardoso (Free State Stars) and Mzikayise Mashaba (Mamelodi Sundowns) were confirmed as squad withdrawals through injury.
The COSAFA Cup takes place from 17 - 30 May.
South Africa will face Botswana in the quarter-final of the competition on Sunday, May 24 at the Moruleng Stadium in the North West Province. Kickoff is at 17:30.
On Wednesday, May 13 Bafana travels to Lesotho to play two training matches against the host nation on Thursday, 14 May and Saturday, 16 May.
South Africa is scheduled to face Malawi in another training match on Friday, May 22 in Rustenburg.
Bafana Bafana squad:
Goalkeepers: Jackson Mabokgwane (Mpumalanga Black Aces), Mondle Mphoto (SuperSport FC), Ricardo Goss (Golden Arrows)
Defenders: Madisha Modjeka (M.Tigers FC), Subisiso Mxoyana (Vasco da Gama), Marc Van Heerden (AmaZulu FC), Siyabonga Nhlapho (Bidvest Wits), Kwanda Mngonyama (Maritzburg United), Clayton Daniels (SuperSport FC), Sibusiso Khumalo (Mamelodi Sundowns)
Midfielders: Cole Alexander (Polokwane City), Thapelo Morena (Bloemfontein Celtic), Thamsanqa Sangweni (Chippa United), Carl Lark (Santos FC), Athenkhosi Dlala (SuperSport FC), Hendrick Ekstein (Kaizer Chiefs)
Strikers: Puleng Tlolane (Polokwane City), Phumelele Bhengu (Thanda Royal Zulu), Gift Matupa (Baroka FC), Moeketsi Sekola (Free State Stars)