Ronan Davies was taken to hospital with severe head and other internal injuries on June 7 and died on June 9.
A subsequent police investigation focussed on a two-day period when he had been cared for by a family friend.
The boy's father had been unable to rouse his son when he was returned.
On Wednesday, South Australia Police said it would be alleged the man caring for the 17-month-old had inflicted the injuries on the afternoon of June 7.
The 30-year-old has been charged with murder and refused bail ahead of an expected court appearance.
Last week, Detective Inspector Mark McEachern said Ronan's injuries would not have been obvious to his father.
"Ronan's been returned home, apparently asleep. We suspect he sustained injuries prior to that," Insp McEachern said.
"We have been provided with an explanation of how Ronan's injuries occurred.
"We're not satisfied with the explanation that's been given to us."
Detectives want to hear from anyone who may have seen the boy in the days before his death.
They were particularly interested in talking to anyone who heard or saw anything involving a young child in Ferguson Street at Glenelg North on the afternoon of June 7, including anyone with dashcam footage of the area from that afternoon.
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