The Argentine striker continued his good form with a brace to grab his team a vital first away win.
New York scored first, converting a penalty kick in the 36th minute. Pa Modou Kah knocked the ball away from Lloyd Sam, but dragged the English winger down with him. Bradley Wright-Phillips put the spot kick away to tie for the lead in the MLS Golden Boot race.
The equalizer came just before halftime, when Urruti's shot from distance took a slight deflection and beat Luis Robles to the near post.
He scored the decider in the 74th minute, capitalizing when a blocked cross fell to him on the far side of the box and firing home from close range.
The win moves Portland to sixth in the West, with a 2-3-7 record. The Timbers are also now undefeated in their last four games. New York is fifth in the East with 3-5-5, its playoff position threatened by a number of teams close behind.