Up to 160 jobs are expected to go as result of cut
Up to 160 ground staff and flight crew members are expected to lose their jobs as a result of the move, to take effect on 27 October.
The announcement came as the company revealed it was to cut back on the number of flights from London to the US and Europe in the wake of the terror attacks on the US.
TBI, the company which operates the Belfast airport, said the action meant its pre-tax profits would fall £1.6m this financial year and £5.3m the following year, in the worst case scenario.
The reduction in passenger air travel following the attacks has affected many airlines.
However, BA admitted its decision had also come because its service of six flights per day between Belfast and London Heathrow was "unprofitable" and had lost £38m over the past four years.
Second blow to industry
The announcement followed another major jobs blow in Northern Ireland this week.
The move also comes as another blow to Belfast International Airport, which is to lose one of its other major carriers, British Midland, to Belfast City Airport, in October.
In a statement, BA said: "The Belfast-London route has a history of unprofitability and in the course of the last four years losses on the route have amounted to £38m.
"The withdrawal of this loss-making service will result in the closure of the airline's operating base, with the exception of cargo at Belfast International Airport."
BA said its subsidiary and franchise operations to and from other Northern Ireland airports would be unaffected.
British Airways General Manager in the UK and Ireland Ian Reid said: "Over the years we have tried hard to maintain the Belfast-Heathrow service.
'Wrong decision'
"However, despite the best efforts of all our staff and support from the local community huge losses have continued."
Ulster Unionist MP for South Antrim David Burnside said BA had made the wrong decision.
Mr Burnside, a former head of public relations for BA, said: "The movement of British Midland to the City Airport in my opinion gave British Airways a great opportunity to market more aggressively on the Belfast International route from Heathrow. That opportunity is being lost."
He added that the route was "vital" for Northern Ireland business and tourism and he is to meet Belfast International Airport managers on Friday to assist them in finding a replacement service.
George Matchett of the GMB union said it was a major blow to the workforce.
He said: "Staff are very disappointed that BA has overreacted to the current situation."
British Airways was the first airline to operate a Belfast to London service when it was launched almost 50 years ago under BEA.