Tomane is expected to be sidelined for six weeks with the left ankle problem, the Wallabies said in a statement.
Vuna, who joined the Melbourne Rebels last year after switching codes from rugby league, will start on the right wing for the Wallabies in the first of three Tests against the Six Nations champions.
Earlier it was announced that Australia had made eight changes to the team that was upset 9-6 by Scotland this week.
Coach Robbie Deans, who - faced with two Tests in one week - always said he would be making major changes, has overhauled his pack.
Loosehead prop Benn Robinson, who missed the last international season with injury, returns in a new front row alongside his New South Wales team-mates Tatafu Polota-Nau, who starts at hooker, and Sekope Kepu.
Rob Simmons replaces the injured Sitaleki Timani in the second row, while Scott Higginbotham moves to the troublesome blindside flanker position to make way for Wycliff Palu to come in at number eight.
Despite the last-gasp defeat in atrocious conditions in Newcastle on Tuesday, Berrick Barnes retains the fly-half berth left vacant by injuries to James O'Connor, Kurtley Beale and Quade Cooper.
The versatile Adam Ashley-Cooper returns to the starting side at full-back, while rugby league convert Tomane was originally retained after being one of six new caps blooded against the Scots.
Pat McCabe also steps up from the bench to replace Mike Harris at inside centre in a midfield partnership with Rob Horne with hard-tackling Anthony Fainga'a relegated to the replacements.
Openside flanker David Pocock has again been named captain in place of lock James Horwill, who was ruled out for the series with a hamstring injury.
Harris, who also made his debut on Tuesday, was named among the replacements and Barnes will take up kicking duties for the Tri-Nations champions.
The series opens at Lang Park on Saturday before Tests on the following weekends in Melbourne and Sydney.
Team: 15-Adam Ashley-Cooper, 14-Cooper Vuna, 13-Rob Horne, 12-Pat McCabe, 11-Digby Ioane, 10-Berrick Barnes, 9-Will Genia; 8-Wycliff Palu, 7-David Pocock (captain), 6-Scott Higginbotham, 5-Nathan Sharpe, 4-Rob Simmons, 3-Sekope Kepu, 2-Tatafu Polota-Nau, 1-Benn Robinson.
Replacements: 16-Stephen Moore, 17-Ben Alexander, 18-Dave Dennis, 19-Michael Hooper, 20-Nic White, 21-Anthony Fainga'a, 22-Mike Harris.