The airline confirmed the incident in a statement by its Communications Manager, Mr Ola Adebanji, a copy of which was obtained by the News Agency of Nigeria (NAN) in Lagos.
According to the airline, the aircraft operated the scheduled Lagos-Johannesburg flight that departed the Murtala Muhammed International Airport at 3:55pm on Tuesday and arrived in Johannesburg shortly before 11pm.
It said engineers of South African Airways Technical facility at the Oliver Tambo International Airport, where the aircraft was scheduled for a routine maintenance check, discovered the body of the stowaway during the inspection phase.
The airline said investigations were ongoing to determine how the stowaway found his way into the aircraft’s main wheel well.