Wallabies back Berrick Barnes has spent the night in hospital after suffering a punctured lung in their Rugby Championship loss to South Africa.

Barnes was initially cleared of a chest injury after the 31-8 loss and returned to the team hotel in Pretoria, but suffered discomfort during the night and was taken back to hospital.

He will remain behind in Johannesburg for the next few days with the team doctor while the side travels on to Rosario in Argentina for their next match.

Adam Ashley-Cooper, who was knocked out just before halftime at Loftus Versfeld, will fly home to Australia.

The other injury concerns - Radike Samo (shoulder), Tatatfu Polota-Nau (neck) and Digby Ioane (knee) - will all fly to Argentina but are no certainties to face the Pumas.

Queensland Reds back Luke Morahan and Melbourne Rebels lock Cadeyrn Neville will join the squad.