Sebetsa-O-Tholemoputso High School in Doornkop, Soweto, has been dealt a double blow.
Khoele collapsed and died at his home on Monday morning, while Zweli Dube (14) died on Friday.
He was on his way home from school.
Education MEC Panyaza Lesufi visited the families to convey his condolences.
Zweli’s mother Puseletso Ntabe (32) told Daily Sun she heard that when her son was struck by lightning, he fell to the ground.
“He tried to run but fell on his face and struggled to breathe,” she said.
Puseletso said Zweli was still alive when she found him lying in a nearby soccer field.
“I told him it was not his time to leave me,” said the mum.
“I just got a new job and had promised to buy him new clothes. Now I am left alone. I will never see my son again.”
Zweli’s grandmum Esther Michini (58) appealed to SunReaders to help bury her dead grandson.
“There’s only one person working in the family and we’re struggling. We want to give him a dignified funeral,” she said.
More than 20 pupils have died since earlier this year.
Lesufi said divine intervention was needed to help curb the number of deaths in schools.