Hooker Jeremy Paul and fly-half Matt Giteau, who left the field before half-time in Saturday's blockbuster at Telstra Stadium, both went to hospital for scans to find out the severity of their injuries.
Paul has damaged his shoulder while Giteau has a sore hip and back.
"Both are extremely doubtful for the next match (against South Africa in Perth next Saturday)," Wallaby coach Eddie Jones said.
"(Centre) Stirling Mortlock has a slight calf strain but we don't think that is too serious.
"There are also a number of guys recovering from heavy knocks - Elton Flatley, Morgan Turinui and Drew Mitchell."
Jones admitted that with Stephen Larkham out for the season with a shoulder injury, Giteau in doubt with the back problem and now Flatley taking heavy knocks to the upper body, the selection of fly-half for Saturday's match in Perth was a concern.
"We will know more about Gits (Giteau) later and we will have a selection hook-up on Sunday night," Jones said.
"Guys that have played Super 12 like Lachlan McKay obviously come into consideration (for the No.10 jersey)."
Jones admitted it was a crucial week for the Wallabies.
"We have just got to get sharper," he said.
"These sorts of games come down to critical incidents where you have the chance to either keep the momentum going on the other side or take it away from them.
"We failed to do that (against the All Blacks) so we have to work on our sharpness so we are mentally right for South Africa."
Jones, who has been forced to use 34 players in the past seven Tests, believes his depleted squad has the ability to hit back hard against the Springboks.
"This squad has got it in it to work hard and put in an emphatic performance.
"You have also got to be good enough to cope with a lot of injuries. We weren't against the All Blacks and that's the test of a team."
Jones admits their second-half performance let the Wallabies down badly.
"We knew we had to play better in the second half than in the first half," he said.
"We needed to raise the intensity in the first 20 minutes of the second half.
"It was always going to be the crucial period of the game.
"The All Blacks score most of their points then and that was the danger period for us.
"We needed to get a score after half-time and when we didn't we were always going to battle."