A Grade 12 pupil was certified dead at Liverpool Secondary School in Benoni, Gauteng, on Thursday.
"The learner collapsed during physical training," Gauteng education department spokesperson Steve Mabona said in a short statement.
There were no further details on the cause of death.
Provincial education MEC Panyaza Lesufi visited the school to convey his condolences.
"Our psycho-social unit team will be dispatched to the school tomorrow [Friday] for necessary counselling," Mabona said.
The tragedy occurred just hours after suspects tried to rob Edenvale High School, also in Ekurhuleni. Two suspects were killed and one was left injured in an ensuing shootout.
ALSO READ: UPDATE: 2 shot dead, 1 injured in Edenvale High School robbery
According to police spokesperson Kay Makhubele: "Police arrived while the suspects were attempting to flee and that is when the shooting started.
"Two suspects were shot dead and one was injured while others made a getaway with two vehicles."
Police do not know how many men managed to flee in the two vehicles.
"The circumstances surrounding the incident will still be investigated," Makhubele added.
The Gauteng department of education further confirmed on Monday that a school governing body member who went to withdraw money for a school trip was robbed of R25 000 at the entrance of Norkem Park High School in Kempton Park.
Nobody was harmed during the robbery.
ALSO READ: Edenvale High School attack: One of the suspects posed as a parent to gain entry
Last Wednesday, a pupil from Dowerglen High School in Edenvale was rushed to hospital after being hit by a stray bullet as suspected cable thieves ran through the school trying to evade security guards.
Upon arrival, Ekurhuleni emergency services found that the 18-year-old boy had sustained upper chest wounds.
ALSO READ: Teenager rushed to hospital after being hit by stray bullet at Dowerglen High School