Will Genia's World Cup hopes have taken a blow with the Wallabies half-back set for surgery on his injured knee.

The veteran played only the first half of Australia's thrilling 24-20 win over South Africa on Saturday night, having limped off at half-time with what scans revealed as bone bruising and ligament damage.

Nick Phipps will start in his place in the second Rugby Championship Test in Argentina next weekend and has the chance to entrench himself at number nine with Genia not expected to be available for selection until the two Bledisloe Cup Tests next month.

Winger Rob Horne has also been ruled out of the squad after straining his calf.

"It's disappointing for Will and Rob to miss this upcoming Test," coach Michael Cheika said.

"They have both made an outstanding contribution to the group this past two weeks, and will continue to remain part of the wider squad from afar."

Nick Cummins and Nic White will replace the injured pair, and will meet the Wallabies squad in Argentina after travelling from the United States, where they have been on a promotional tour ahead of the forthcoming Test in Chicago.

Also included are hooker James Hanson and prop Tetera Faulkner, who come into the group to further bolster a pack that was soundly beaten by South Africa, while Rory Arnold and Taqele Naiyaravoro have dropped out.

Veteran Matt Giteau also came away from the Springboks clash worse for wear, copping a hit to the nose that forced him off the field for a stretch in the second half with blood gushing from his face, but it was not enough for him to miss the plane to Argentina.

In his first Test match in four years, Giteau looked on-song but it was a rocky night overall for the Wallabies' much talked about 9-10-12 axis with Genia and Quade Cooper.

Wallabies squad to face Argentina Adam Ashley-Cooper (Waratahs), Kurtley Beale (Waratahs), Quade Cooper (Reds), Nick Cummins (Force), Tetera Faulkner (Force), Scott Fardy (Brumbies), Israel Folau (Waratahs), Bernard Foley (Waratahs), Matt Giteau (Toulon), James Hanson (Reds), Scott Higginbotham (Rebels), Greg Holmes (Reds), Michael Hooper (Waratahs), James Horwill (Reds), Sekope Kepu (Waratahs), Tevita Kuridrani (Brumbies), Stephen Moore - Captain (Brumbies), Drew Mitchell (Toulon), Ben McCalman (Force), Sean McMahon (Rebels), Dean Mumm (Waratahs), Nick Phipps (Waratahs), David Pocock (Brumbies), Tatafu Polota-Nau (Waratahs), Scott Sio (Brumbies), Rob Simmons (Reds), Will Skelton (Waratahs), James Slipper (Reds), Matt Toomua (Brumbies), Joe Tomane (Brumbies), Nic White (Brumbies)

Dramatic win ... Tevita Kuridrani celebrates with Israel Folau and Scott Fardy after the Wallabies' late game-winning try against the Springboks. ( Getty Images: Chris Hyde )

SCOREBOARD: AUSTRALIA 24-20 SOUTH AFRICA 24-20 at Lang Park, July 18 2015 143 Total runs 83 62% Possession 38% 50 Phase sets 46 9 Line breaks 3 Wallabies: Ashley-Cooper (32 mins), Hooper (73 mins), Kuridrani (81 mins) tries, Cooper 1 pen goal, 2 convs, Giteau 1 conv. Springboks: Etzebeth (37 mins), Kriel (44 mins) tries, Pollard 2 pen goals, 2 convs.

Cooper's stocks may have fallen to a degree following an unconvincing performance at five-eighth, and the Wallabies looked a more potent outfit when he was swapped with Matt Toomua for the last 10 minutes.

The 27-year-old had an indifferent night and failed to provide the polish that many were hoping he would bring to Australia's attack.

But he remains in Cheika's good books, even accounting for his daring behind-the-back flick pass that so easily could have resulted in a Springboks try deep into first-half red time.

"Fine," Cheika said when asked how the coaching box reacted to it.

"If Tevita (Kuridrani) takes that ball, he's away ... we score at the other end of the field at half-time.

"I've got no issue with that one at all.

"I'm never going to tell a player not to do that ... because he can do it and made the pass. I've seen him do it at training so there's no reason why he can't.

"(Kuridrani) was probably shocked it came out because it was an incredible ball."

AAP