Both new and existing workers will contribute 2 percent of their pay to health care costs, a significant change that could figure prominently in future negotiations throughout the region. Members of New York City’s municipal unions, for instance, generally do not pay for health care.

“They brought the union into the 21st century with regard to health care,” said Mitchell Moss, the director of the Rudin Center for Transportation Policy and Management at New York University. “The vast ridership is paying some part of their health care cost. It’s inevitable that workers were going to have to start paying a portion of their health care.”

The deal must be approved by union members and the authority’s board. The contract is retroactive to June 2010, and expires in December 2016.

Though Mr. Cuomo, a Democrat, had initially kept a public distance from the negotiations — at an authority he oversees — transportation experts had long expected him to intervene.

Last week, after Mr. Cuomo suggested that Congress was better suited to weigh in on a possible strike, Mr. Prendergast went to Washington to discuss the potential for a strike with lawmakers. Members of both parties said they were unlikely to get involved, which some officials viewed as a blow to union leaders who might have expected Congress to intervene on their behalf during a strike.