Australia, full of confidence after an unchanged XI whitewashed England 5-0 in the Ashes, are also sweating on batsman Shaun Marsh, who has a calf strain, and the fitness of paceman Jackson Bird.
Marsh will not travel to South Africa as scheduled but will remain in Perth for further treatment, before a decision is taken on whether he will join the tour.
Bird will also stay in Australia and return to bowling to determine if he has recovered sufficiently from back problems.
Faulkner, who hurt his right knee in the final one-day international win against England in Adelaide on Sunday, will be replaced in the 15-man Test squad by Moises Henriques.
The New South Wales all-rounder plays in Wednesday’s first of three Twenty20 matches against England while South Australian Kane Richardson joins the squad as cover.
“Moises Henriques has shown some good form recently with both bat and ball and he provides a good fit when looking to replace James,” said national selector John Inverarity.
“The NSP (national selection panel) is hopeful that James will be fit for the three Twenty20s in South Africa and for the ICC World Twenty20 following as that is a key tournament for him.” “Kane Richardson has been called to Hobart to replace James in our Twenty20 squad. He has shown promise as a shorter-form young cricketer and will gain from the experience of being involved,” Inverarity added.
The bulk of Australia’s squad was due to fly out to South Africa on Wednesday.
The first Test starts on February 12 at Centurion, with the second Test in Port Elizabeth from February 20 and the third and final Test in Cape Town on March 1.