The girls, aged five and eight, were found in an abandoned building in Atteridgeville on Friday.
Police officers were called by members of the community and “on arrival at the scene made the gruesome discovery”, police spokesperson Brigadier Mathapelo Peters previously told News24.
At the time, no one had come forward to report missing children, Peters said.
“The bodies were burnt beyond recognition and, at the time of discovery, the deceased were unknown, with little to no information on the circumstances surrounding their gruesome deaths,” she said.
“A priority investigation unfolded… and within about two days police had valuable information that assisted in determining that the deceased were siblings, and also led to the arrest,” Peters added.
The 25-year-old woman was arrested at the Stadium Plaza shopping centre in Atteridgeville on Sunday.
She appeared in the Atteridgeville Magistrate’s Court on Tuesday. The case has been postponed to 15 February and the woman remains in custody.