ALBANY, N.Y. — The state Legislature granted Mayor Bill de Blasio two years of additional control over New York City’s schools Thursday, a day before the policy was to expire, ending the uncertainty over leadership of the nation’s largest school system.

The resolution of the issue came at the end of a special two-day legislative session, with the state Assembly giving its approval early Thursday and the state Senate following suit when it reconvened later in the day.

The squabble over mayoral control had spilled over from the regularly scheduled legislative session, which ended last week, after Republican and Democratic lawmakers deadlocked over whether de Blasio’s control should be linked to an increase in the number of charter schools.

In the end, the Democrats in the Assembly, who did not want more charters added, prevailed, securing the two-year extension without approving additional charter schools.

Instead, they addressed a set of upstate considerations, including additional money for flood victims on Lake Ontario; access to more money for road and well construction in the Adirondack region; and a relief package for Vernon Downs, a racetrack and casino near Utica.

Governor Andrew Cuomo, who had asked that the session be convened Wednesday, is expected to sign the omnibus bill. He had initially said lawmakers returning to the Capitol would solely be concentrated on mayoral control as the deadline loomed, but soon it became apparent that a multitude of outstanding issues would be raised by lawmakers, given the so-called extraordinary session.

Cuomo himself earned passage of an agreement close to his own heart, the renaming of the Malcolm Wilson Tappan Zee Bridge, north of New York City, in honor of his father, former governor Mario Cuomo.