Starting in 1996, motorists in New York State will be able to use the Gov. Thomas E. Dewey Thruway without paying tolls, under the terms of an agreement signed here today by representatives of the Federal Highway Trust and state officials.

The annual saving for truck and passenger car owners, assuming tolls in 1996 would be the same as now, would be $155 million. Under the agreement, the Federal Government will contribute $9.8 million next year and more in subsequent years to repair and rehabilitate the 559-mile road linking New York City, Albany and Buffalo. In the next 14 years, the total Washington contribution to repairing the Thruway may reach $550 million, officials said.

Bonds Will Be Paid in 1996

In return, the New York State Thruway Authority agreed that in 1996, when all its bonds are paid off, it would recommend to the State Legislature that the authority be abolished and the road be made toll free.

Under the terms of the agreement, if the Legislature does not eliminate the tolls, it must repay to the Federal Government all funds contributed by the Highway Trust. Officials here said such a repayment was most unlikely.