A truck delivering food to Lekgolo Primary School crashed into a wall which then collapsed on two pupils on Wednesday, the Limpopo Education Department confirmed.
Education Department spokesperson Sam Makondo said two other pupils were seriously injured and rushed to Kgapane Hospital.
Provincial police spokesperson Brigadier Motlafela Mojapelo told News24 the deceased were aged just five and seven.
He said the truck was believed to have been reversing before hitting the wall.
"We have opened an inquest docket and will check on the whole circumstances surrounding the incident."
Provincial Education MEC Polly Boshielo said she was saddened by the news and was rushing to the scene.
"The department's psychosocial unit has been dispatched to start with the work of providing the necessary trauma counselling to learners, educators, support staff and the bereaved families," said Makondo.