Baxter was dealt a blow following the withdrawals of Bongani Zungu and Themba Zwane, with Hlompho Kekana the latest to have been confirmed unavailable, due to injury.
The trio all picked up ailments in their recent fixtures this past weekend, and have not made the trip with the team to their base in Durban.
Orlando Pirates winger Vincent Pule, SuperSport United utility midfielder Aubrey Modiba and Mamelodi Sundowns workhorse Tiyani Mabunda have since been called up to the camp.
Pule is the only uncapped player to be called up in the current camp, and becomes the second Pirates player after left-back Innocent Maela.
Modiba has been an ever-present for Matsatsantsa, and was part of Baxter's recent squads as well as the junior national team setup, while Mabunda also featured during the World Cup qualifying campaign last year.
South Africa and Libya will square off in a top-of-the-group clash at the Moses Mabhida Stadium on Saturday afternoon. Kick-off is set for 15h00.
Meanwhile, Nigeria will travel to Seychelles in Group E's other clash, which is also set to take place on the same day (14h30 - SA time).