Polota-Nau missed the British and Irish Lions series with a broken arm and his return has now been delayed by two weeks because of a hamstring problem.
Kimlin had an excellent season with Super Rugby runners-up ACT Brumbies but will miss six weeks after surgery on a broken thumb he suffered in the semi-final victory over the Bulls in Pretoria last month.
The 28-year-old, who won two caps in 2009 and can also play in the second row, was included in Ewen McKenzie's first squad as Wallabies coach despite having elected to move to French club Grenoble for next season.
McKenzie has elected to bring just one replacement into the squad with uncapped front row forward Albert Anae, who can play both hooker and prop, getting the call-up.
"Albert is still young for a front-rower but his versatility is a real asset," said McKenzie, who coached Anae at the Queensland Reds.
"You're always searching for players with a lot of potential and Albert is a guy who will learn plenty from being part of the national environment."
The Rugby Championship starts next week when Australia host world champions New Zealand in Sydney and South Africa take on Argentina in Johannesburg.