Detectives called for help from the public a week after the bones were discovered by a passer-by in bushland close to Wynarka, a small town about 130 kilometres (80 miles) southeast of Adelaide.
The girl's identity is not known and a man aged about 60, seen carrying a suitcase in the area some weeks ago, is being sought by police, Detective Superintendent Des Bray said.
The girl had fair hair and was aged between two to four when she died, Bray said, adding in a statement that "for reasons I'm not going to disclose we are confident that this child was murdered".
Bray said the girl could have died some years ago as the clothing she was found with, including a black tutu, a pink shoe, a "Dora the Explorer" purple top and red sports shorts, dated as far back at 2007.
Although police had contacted all missing persons units and homicide squads across the vast country, there was no-one they had a "strong focus on".
Investigators also did not know where the girl died, but believe she was "killed elsewhere and her remains put into the suitcase and shifted in relatively recent times", Bray added.
Police said the black suitcase, which had faded to grey by the time it was found, was left behind a bush, and at "some stage" the remains were tipped out and the bag placed in full view of the road.
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