The baby is 7-weeks-old.
The couple were arrested at the weekend after staff at the Linmed Netcare Hospital, who had been treating the little one for bronchiolitis, noticed his injuries, The Star reported.
The child sustained a head injury which could have an effect on his development, a doctor said.
The couple was released on bail of R3 000 each, angering child rights activists.
They will be back in court on 11 July. Meanwhile, their child has been taken to a place of safety.
News of the baby’s alleged abuse comes just after it was reported that a man in Beaufort West was arrested for torturing his girlfriend’s 2-year-old child.
The man is alleged to have slapped and kick[ed] the boy in the face, burned his feet with boiling water, put a cement brick on the boy's chest and stamped his feet on it and also forced the boy to eat his own faeces.