The matter was postponed to May 5, for further investigation.
The accused, who is in his twenties, is said to be the father of the deceased.
He is facing charges of murder and kidnapping.
The case will potentially be tried in the High Court, provided investigations are completed.
The suspect will remain in custody.
According to Constable Nkemeleng Mabula, from Dawn Park SAPS, the child disappeared on January 24 and was found the following week near Zonkizizwe, Boksburg.
READ STORY: Three-year-old girl found with her head cut off
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