The Wallabies will return to Australia for two Tests against world champions South Africa with their pride dented by a seven-tries-to-two 48-17 flogging - easily their biggest ever loss to the Pumas.

On the back of the thumping bonus-point victory, the Pumas moved to the top of the four-nation standings after the Springboks and All Blacks also split their results over their two games.

The Wallabies were outplayed in every department in San Juan with Cheika breathing fire into his Pumas side following their opening Test loss in Mendoza.

He switched up his game plan with Argentina using a contestable kicking game to expose the inexperience of Australia's back three and force a number of costly errors.

The home side piled on the pressure in a physical performance with the Wallabies, missing key men such as skipper Michael Hooper through personal leave and injury, bereft of answers.

Stand-in skipper James Slipper post-match said they were eager to get home after a "rough tour".

The Australians' pattern of slow starts continued, gifting two tries in the opening six minutes with the home side racing to a 26-10 half-time lead, but this time the Wallabies were unable to mount a fightback.

"Massive disappointment," was the assessment by Wallabies coach Dave Rennie.

"We conceded four tries with kicks in behind us and certainly got dominated in the collision area.

"We want to earn the respect of the country and you don't do it with a performance like that."

Australia had a James O'Connor try, which would have given them the lead, disallowed in the 20th minute in a baffling refereeing decision and the Pumas scored minutes later in 14-point swing.

Referee Karl Dickson and the TMO deemed an earlier clean-out by Slipper was illegal.

It proved a turning point with the remainder of the game almost one-way traffic.

"It was just the way they saw it - it was a pretty important call as at the time it would have put us in front but you've got to take that," Rennie said.

"We created opportunities that if you nail you stay in the game and can build some pressure, but we couldn't buy a trick, especially second half."

Rennie said his team paid for poor decision-making, after they threw passes that weren't on with winger Jordan Petaia one of the culprits.

The shining lights were powerhouse backrower Rob Valetini and winger Marika Koroibete, who pulled off a try-saving tackle late in the first half.

The Australians should have hookers Dave Porecki and Folau Fainga'a and centre Hunter Paisami, who all suffered concussion on tour, available to meet the Springboks in Adelaide on August 27.

Outside back Andrew Kellaway and props Angus Bell and Scott Sio, who didn't travel due to injury, are also set to return.

There's no word on when Hooper, who flew home for mental health reasons, will return to the squad.

While he admitted lack of cohesion hurt his team Rennie said the returning players wouldn't be a quick fix.

"We had a good enough side to do the job ... whoever pulls the jersey on has got to front and we weren't good enough," he said.

"We've got to be better and we've got to own that - it's on us as coaches and it's on the players."

Australian Associated Press