In a statement, the South African Police Service said the boy’s father was not at home but that his mother heard the gunshot.
A former security officer apparently left his firearm in a bag that was hung against a wall in his room.
The victim and her baby were transported to hospital by ambulance for medical attention.
Lihle Mmusi went missing on Friday under mysterious circumstances.
Chantel Makwena was reportedly raped, beaten to death with a rock and dumped in an outhouse near her family’s PE home.
The alleged rapist is an active member of the DA in Borcherds, which was confirmed by the party.