The ARU asked SANZAR to investigate the issue after admitting it was a surprise to see so many star names ruled out of the tournament's opening clash in Sydney on July 23.
But the SARU claim the issue has now been put to bed after SANZAR saw nothing untoward in the selection.
"Australia asked for an enquiry, an enquiry has been done by SANZAR and we have given our reply. SANZAR is happy with the result, and in the words of (SANZAR CEO) Greg Peters, it has been dealt with," said SARU CEO Jurie Roux.
"I did get a query from Greg Peters in that regard. I provided him with the list of injured players and the medical assessment - obviously not the detail, that's our information and that's privileged information…they were happy with that."
A whole host of big-name Boks won't feature in Sydney in a fortnight or against the All Blacks in Wellington a week later, with the likes of Victor Matfield, Bakkies Botha, Bryan Habana and Fourie du Preez among them.
Also unavailable for at least the first two games of the shortened competition are squad regulars Schalk Burger, Tendai 'Beast' Mtawarira, Juan Smith, Bismarck du Plessis, Andries Bekker, Jannie du Plessis, Gurthrö Steenkamp, Jean de Villiers, Butch James, JP Pietersen, Frans Steyn and Jaque Fourie.
But while the extent of the list has raised suspicions that the Boks may be resting players for the home leg of the Tri Nations and the forthcoming World Cup, Roux insists the SARU's conscience is clear.
"We're more than happy that what we have on the table at the moment was a proper process and that we've followed due process," added Roux.
"We've been open and honest in it. We've got a professional team and the professional judgement from our medical staff is that these players are not fit to play," he added.
John Smit leads the Boks' 27-man squad Down Under, with Ulster duo Ruan Pienaar and Johann Muller the only overseas-based players included.
Smit, Pienaar and Muller are among just nine players who featured in the Test series against the Lions two summers' ago, with Adrian Jacobs, Odwa Ndungane, Wynand Olivier, Heinrich Brüssow, Ryan Kankowski and Chiliboy Ralepelle the others.
The Boks met up in Johannesburg for their first squad session yesterday and will head to Australia this Friday.
South Africa squad for Tri Nations away leg
Forwards: Heinrich Brüssow, Jean Deysel, Dean Greyling, Alistair Hargreaves, Ryan Kankowski, Werner Kruger, Ashley Johnson, Johann Muller, Coenie Oosthuizen, Chiliboy Ralepelle, Danie Rossouw, John Smit, Deon Stegmann, Adriaan Strauss, Flip van der Merwe
Backs: Gio Aplon, Bjorn Basson, Juan de Jongh, Adrian Jacobs, Elton Jantjies, Patrick Lambie, Charl McLeod, Lwazi Mvovo, Odwa Ndungane, Wynand Olivier, Ruan Pienaar, Morne Steyn
Injured players unavailable for selection
Duane Vermeulen (knee), Fourie du Preez (knee), Schalk Burger (thumb), Victor Matfield (calf and neck), Frans Steyn (ankle and back), Jaque Fourie (groin), Jean de Villiers (groin), BJ Botha (knee), Juan Smith (Achilles), Willem Alberts (shoulder), Bismarck du Plessis (shoulder), Andries Bekker (shoulder, groin and ankle), Jannie du Plessis (knee), Francois Louw (clavicle), Gurthrö Steenkamp (forearm), Francois Hougaard (ankle), Butch James (knee), JP Pietersen (back), Tendai Mtawarira (hamstring), Bryan Habana (shoulder), Bakkies Botha (knee)