The Sweden-based forward was among three players that did not arrive in Durban with the rest of the team on Monday, along with goalkeeper Darren Keet and defender Anele Ngcongca, who have since arrived.
“Unfortunately we received a letter that says he (Mahlangu) played a lot of games and needed a rest,” Mashaba told reporters after training on the outer fields of the Moses Mabhida Stadium on Tuesday morning.
“That is what is happening and we cannot do anything about it.”
Another midfielder Sibusiso Vilakazi is also not with the squad after failing to recover from a toe injury.
South Africa play Sudan in the coastal city on Saturday, before facing Nigeria in Uyo next weekend.
Both matches serve as qualifiers for next year’s Africa Cup of Nations, which Bafana Bafana will qualify for should they win against the Sudanese and Group A rivals Congo lose to the Nigerians.