Police said they had arrested a 37-year-old man and a 36-year-old woman who were known to the child.
The girl was found unresponsive at a Coomera residence in April 2022.
Detective Inspector Paul Fletcher said the circumstances surrounding the case were "particularly confronting".
"The investigation into the death of this young girl has been one of the most heart-wrenching and complex we've had to conduct," he said in a statement.
"From the moment the investigation commenced, our priority has been to seek justice for this innocent child who was tragically failed by those known to her.
"It is deeply distressing to investigate the death of any child but the circumstances surrounding this case have been particularly confronting for our officers."
Det Insp Fletcher said the case had also impacted the Gold Coast community.
"We understand the grief and pain this has caused the community, and we hope these arrests bring some level of comfort to those who knew and loved this young girl," he said.
"While nothing can undo the tragic loss of life, we are committed to ensuring justice is served."
The man and woman were to face Southport Magistrates Court on Tuesday.Â
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