The stand off is still struggling with the shoulder injury which prevented him playing in the final Test against the Lions.
Australia's Tri-Nations begins in Pretoria on 28 July and Manuel Edmonds of New South Wales has been placed on standby for the World Cup-winning fly-half.
An Australian Rugby Union statement said: "Larkham has been ruled out of the first Tri-Nations match in Pretoria due to a nerve problem in his shoulder but he's considered a strong chance to play in game two against the All Blacks in Dunedin on 11 August."
Queensland's Elton Flatley took Larkham's place in the third Test against the Lions, a game Australia won 29-23.
"I have spoken to a neurosurgeon.
"He was very happy with the progress of my arm but he said it will probably be another couple of weeks before it was fully back to playing condition.
"At this stage I will be back with the team in the lead-up to the New Zealand game."
Full squad
Backs: George Gregan, Chris Whitaker, Elton Flatley, Stephen Larkham (Manuel Edmonds on standby), Joe Roff, James Holbeck, Nathan Grey, Graeme Bond, Daniel Herbert, Andrew Walker, Chris Latham, Matthew Burke.
Forwards: Nick Stiles, Bill Young, Michael Foley, Brendan Cannon, Rod Moore, Ben Darwin, David Giffin, John Eales (captain), Justin Harrison, Mark Connors, Owen Finegan, Matt Cockbain, George Smith, Phil Waugh, Toutai Kefu, David Lyons.