Steyn clutched his right shoulder on the follow-through when bowling at the WACA before lunch and promptly left the field to head to hospital for scans.
"Preliminary scans .... confirmed a new fracture of the bone in the shoulder joint," Cricket South Africa said.
"He will take no further part in the match (he will bat if absolutely necessary) and the series, and will return to South Africa to see a shoulder specialist who will advise on an appropriate plan of action."
CSA said the 33-year-old would probably need surgery. No replacement has been decided.
Steyn broke the same shoulder nearly a year ago, forcing him out of tests against England.
The loss of the pace spearhead is a hammer blow for the tourists, who play two more tests against Australia in Hobart Adelaide.
The remaining bowlers rallied brilliantly in Steyn's absence, dismissing Australia for 244 on Friday before the Proteas batsmen pushed to 104-2 at stumps and a lead of 102 runs.
Steyn's absence may be felt more keenly if South Africa bowl again in Perth, with Vernon Philander and 21-year-old Kagiso Rabada to shoulder the pace burden alone.
Morne Morkel, who missed the New Zealand tests with a back injury, was rested for Perth and is likely to slot in for the remaining tests. Kyle Abbott is the other back-up seamer in the squad.
(Reporting by Ian Ransom in Melbourne; Editing by Ed Osmond)
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