Bafana Bafana have been forced into an almost complete team overhaul with 11 of the original 18-man squad to face the Socceroos pulling out.
Some of the new call-ups are believed to have left the country on holidays after a hectic domestic season and have yet to be reached.
Others have expressed surprise at their inclusion.
The South Africa national team was meant to fly out for Australia on Wednesday but have rescheduled their flight for Thursday as football officials scramble to arrange travel documents for late call-ups.
The side is due to play Australia in their World Cup farewell friendly on Monday before taking on New Zealand four days later.
But the mass exodus of players has left the team's plans in a shambles.
Star players including Crystal Palace-based midfielder Kagisho Dikgacoi and FC Rostov defender Siyanda Xulu are among those who have pulled the plug on the tour.
"There have been a couple of withdrawals unfortunately," Coach Gordon Igesund told Sport 24 at OR Tambo International airport on Tuesday.
"Of the 18 players called up, 11 have withdrawn through injury and clubs not wanting to release players.
"With some of the players, we only found out last night (that they had withdrawn)."
Igesund, who was banking on a good showing against the Aussies and Kiwis to cement his position as national team coach, said it was frustrating for everyone involved.
"If I look at the players that are missing, nine of them would've started the match. It becomes difficult with only two days to prepare."
Not all the new call-ups have met with success. Bidvest Wits midfielder Sibusiso Vilakazi was brought in to replace Andile Jali only to succumb to injury, forcing Igesund to find another replacement in 31-year-old veteran Teko Modise.
Kermit Erasmus was called-up to replace Bernard Parker but is believed to be holidaying in Holland with his phone turned off.
"This thing has come at a bad time for us," the beleaguered coach said.
"The players are human beings and need to go on holiday after a long season. It's always tough to get a late call-up."
He said he had not spoken directly to the 23-year-old Orlando Pirates striker.
"If Kermit is on holiday in Holland I have to respect that."
Meanwhile, Socceroos coach Ange Postecoglou has downplayed the impact of facing a massively understrength side in the penultimate match before the World Cup kicks off in Brazil.
"We will wait and see what happens," Postecoglou told the Daily Telegraph.
"From my perspective, I’m not worried about them. It’s about our preparation.
"Whatever team they put out it will still be a good test for us.
"Every game leading up to the start of the cup is important."