The boy was found under his desk with the string around his neck on Monday, department head Nkosinathi Sishi said.
His desk was next to a window. He tied the piece of string to the window and the other end around his neck. Sishi said the boy was still alive when he was taken to a clinic, but died later.
KwaZulu-Natal police were investigating.
“Foul play is not suspected at this stage,” Colonel Jay Naicker said.
Sishi said he visited the school and the boy’s family on Tuesday. The department had provided counselling for the family, staff and children at the school.
“This is the worst… we’ve never had an incident of this nature,” he said.
A number of pupils have died at schools this month. Last week, an eight-year-old girl died after she was kicked and beaten, allegedly by three bullies at a Soweto primary school. Lebohang Makala reportedly returned home from school on February 14 limping and with swollen legs.
She told her mother Martha Makala that three boys hit her for no reason while she was playing with other girls at the Batsogile Primary School. Apparently no teachers were at the school at the time, and other children could not find anyone to help Lebohang, who lay helplessly on the ground.
The girl was taken to hospital for X-rays and sent home. On Thursday she was in pain and her family took her back to the hospital, where she died on Friday. The Gauteng education department and police were investigating.
Earlier this month, a Grade R pupil died after being run over by a lawnmower at another Soweto primary school. The five-year-old pupil was declared dead on arrival at hospital.
The Gauteng education department would investigate whether any safety regulations or policies were breached.
In Mpumalanga, a Grade nine boy was stabbed to death, allegedly by another pupil at a secondary school in Zoeknog this month. Police said the two pupils had been in an argument. The alleged killer handed himself to police in Acornhoek.