The later of the two departing overnight flights from South Africa to London will no longer be in operation from April 20.
Instead, the airline will operate the single flight departing Johannesburg early in the evening before setting off on the return leg from the UK.
SAA chief executive Vuyani Jarana said: “We have decided to focus on those areas of our business that will enhance our efficiencies, bring more value to our customers and produce improved overall performance of the airline.
“Network optimisation is one such area that can contribute towards containing our costs and we introduced some initiatives that must yield dividends to return the business to commercial sustainability in the shortest time possible.”
A spokesman for the airline said profitability on the route is expected to grow further thanks to the decision to start operating an Airbus A330-300 on the route from March 25, as opposed to the A330-200 currently in use.
The change of aircraft means there will be 46 seats available in business class, as opposed to the 36 currently on offer, while the aircraft will have space for 249 passengers in total, 27 more than present.
Improved technology means the new aircraft, five of which were delivered last year, will be more efficient and therefore more profitable.
Jarana added: “This will afford customers a significantly improved on-board business and economy product, with state-of-the-art technology, increased comfort and capacity.”
He said the airline has leased out the second Heathrow slot, meaning the option remains to reinstate the flight once the lease period comes to an end.
However, a spokesman refused to comment on industry speculation that British Airways have picked up the slot.