A thug held him at gunpoint before plunging a knife into his thigh.
The airline’s veteran pilot was rushed to hospital for immediate treatment.
He had gone jogging with a crew member during downtime while on a stopover in Johannesburg, The Sun said.
The newspaper claimed they broke strict BA rules by leaving the security approved compound which houses their crew hotel.
Much of the South African city is off limits due to the notoriety of crime-ridden Johannesburg.
The BA facility houses a hotel in the Melrose Arch neighbourhood, as well as a number of luxury amenities such as a bowling alley.
The injured captain was allowed to leave hospital after treatment and jetted home earlier this week.
Separate crews were found to bring home the plane from South Africa and passengers were not informed.
The Foreign Office’s advice to Brits travelling to South Africa states: “There is a high crime rate, including carjacking, house robbery, rape, sexual assault and murder.
“Violent crime can take place anywhere, including in tourist destinations and transport hubs.”
BA told the Standard: “We provided support to our colleagues who have since returned to the UK.”
