Airlink has bases in Johannesburg, Cape Town and Durban and serves cities in 14 countries, including South Africa, Zimbabwe, Zambia and Namibia.
Airlink, a former South African Airways franchise partner, has moved closer to BA following the severing of its relationship with SAA in a row over payments. SAA has also ceased flying to the UK.
The agreement means BA customers will be able to connect to their final destination via Cape Town or Johannesburg on a single ticket.