Carter also sidelined
Australia were dealt a double blow in the wake of their impressive first Test win over France in Brisbane at the weekend.
Wallaby captain Stephen Moore has been ruled out for the rest of the year with a serious knee injury.
Scans revealed that Moore ruptured his anterior cruciate ligament and medial ligament in the opening minute of their 50-23 win over France in Brisbane.
And lock Sam Carter is out for the remainder of the June Tests, with scans revealing that he suffered a syndesmosis injury to his left ankle.
"I'm going to need some surgery to repair my ACL/MCL. Will get it fixed up and look to go again," Moore tweeted.
The 92-Test hooker injured his left knee after falling awkwardly while making a tackle on French flank Bernard Le Roux.
Moore, 31, captaining Australia for the first time, attempted to play on but was forced off the field by his injury, and was replaced by Tatafu Polota-Nau.
Flank Michael Hooper took over the Wallaby captaincy and led from the front in a superb display.
Moore's injury is the latest in a series that struck down James Horwill, David Pocock and Will Genia in 2012, when the Australian captains were all injured in quick succession.
Moore will also miss the final games for the Brumbies, who are lying fourth in Super Rugby with three games left to next month's top-six play-offs.
Carter will commence his rehabilitation immediately with a view to returning to the playing field during the later stages of the Brumbies' Super Rugby campaign.
A decision on replacements into the Wallabies 32-man squad will be made later on Sunday.
Wallabies coach Ewen McKenzie sympathised with Moore and Carter.
"We all witnessed during the week just how passionate Stephen and Sam are about representing their country, so it's disappointing on a personal level to lose them through injury after just one game," McKenzie said.
"For Stephen, I couldn't have been more pleased by how he carried himself as our captain during the week, and with the contributions he was making on behalf of the team.
"I wish him the best with his rehabilitation.
"He'll work hard to get his knee right and will play a major role in our preparations for the Rugby World Cup in 2015.
"For Sam, he's now got a taste of what Test Rugby is all about, and I've got no doubts he'll continue to work hard to be available when we select our Rugby Championship squad next month."