Financial assistance, believed to be in the region of £9m over three years, will be provided.
Most of the money is coming from Stormont.
The BBC has established United was set to axe the route next month, believing its aircraft could be more profitably used elsewhere.
The managing director of Belfast International Airport, Graham Keddie, said: "Two weeks ago we had lost it.
"It was a Northern Ireland team effort to get it back."
Economy Minister Simon Hamilton said the rescue package had the backing of the executive.
"It is public money being spent to ensure we keep this very important route in place," said Mr Hamilton.
He said the route was crucial to attracting US-inward investment.
Northern Ireland politicians lobbied their counterparts in the US as part of the effort to have United re-think its initial decision.
DUP MP for North Antrim Ian Paisley said: "Losing this route would have been a blow to the prestige of Northern Ireland.
"Imagine the outcry if this had been lost."
The Ulster Unionist MP for South Antrim, Danny Kinahan, added: "This is an excellent example of what can be achieved when political differences can be put aside."
A rescue deal has been agreed to prevent US airline United ending its daily service between Belfast and New York.