The officer was attempting the traffic stop on the northbound Cross Island Parkway when he lost control just before 3 a.m.
The cruiser flipped, coming to a rest just over the county line in Queens.
The officer was taken to North Shore University Hospital for treatment of non-life threatening injuries.
It was not immediately known why the officer, who is assigned to Nassau County's Third Precinct, was attempting to pull over the vehicle. That driver got away.