McCarthy and Ndlovu suffered a hamstring and a dislocated shoulder respectively in South Africa's 1-0 loss to Brazil on Friday at the Estadio do Morumbi Stadium in Sao Paolo Brazil.
The duo has since been released from the squad.
"It is sad that we have lost the two players but it is part of the game there's not much we can do but wish them a speedy recovery," Igesund said.
"We have only one training session on Monday so it doesn't help to bring in any replacements.
"The situation also gives me a chance to see and work with the players in the squad who did not get an opportunity against Brazil and I am confident they will raise their hands when given the opportunity."
England-based midfielder Kagiso Dikgacoi has also been released to return to his club, leaving Igesund with 21 players to work with.
Bafana has already arrived in Nelspruit to complete preparations ahead of the Mozambique encounter at the Mbombela Stadium.