According to the Airports Company South Africa (Acsa), the matter falls under police investigation due to a possible criminal factor connected with such an incident.
Details of how the two got on the flight, where precisely they were located in the plane and their nationalities were not available, Acsa spokesperson Colin Naidoo said.
The last incident of a similar kind to occur in South Africa was 10 years ago, involving the same airport, he said.
Security had been heightened at OR Tambo since the latest incident, Naidoo said.
The surviving man is in a critical condition and under treatment in a London hospital having been found unconscious on the flight yesterday after the plane had landed, according to UK police.
The body of a man had been found on the roof of an office under the flight path to Heathrow airport and authorities were working to determine if he fell from the same plane.
The man found alive is believed to be 24 and was found in the undercarriage of the plane, police said.
The possibility that the two men were on the same plane was “one of the lines of inquiry”.
Police were called about the suspected stowaway at 8.28am and about the body at 9.35am yesterday.
The flight from Johannesburg to Heathrow takes 11 hours and outside temperatures during the journey could fall as low as -60o C.
A British Airways spokesperson said: “We are working with the Metropolitan Police and the authorities in Johannesburg to establish the facts surrounding this very rare case.”
The body was found on the roof of the offices of notonthehighstreet.com, an online retailer in Richmond, a wealthy southwest suburb of London.
“Officers and the London ambulance service attended and found the body of a male on the roof of the premises,” the
company said in a statement.