In the first ever game between these two sides the world No 23 South Americans scored a rare goal four minutes into the second half at Sports Illustrated Stadium.
Nilson Angulo was credited with the opening goal that snuck in past goalkeeper Max Crocombe's post off an assist from Gonzalo Plata. It was Angulo's first goal for his country.
Leonardo Campana scored the second seven minutes before full-time, also his first for Ecuador.
Ecuador have now only conceded five goals in their last 15 games, while keeping yet another clean sheet. This victory stretched Ecuador's unbeaten run to 15 games.
Crocombe's efforts between the posts stopped Ecuador from capitalising on even more of their chances.
Meanwhile, the New Zealanders were unable to truly test the opposition keeper.
All Whites coach Darren Bazeley made changes to the starting side for the second game of the international window with Tyler Bindon replacing Michael Boxall in defence, Alex Rufer and Ben Old started in the midfield for Joe Bell and Matthew Garbett with Ben Waine also getting his chance up front.
Marko Stamenic skippered the side with Boxall on the bench and regular captain Chris Wood missing the All Whites' games this month.
New Zealand defender Bill Tuiloma was forced from the field with a leg injury just before half-time with Storm Roux called on as the early replacement.
The All Whites end the calendar year with three wins, six losses and a draw.
On December 6 the Football World Cup draw will be held in Washington DC and the All Whites will find out who they will play, and where, at next year's tournament co-hosted by United States, Canada and Mexico.
The All Whites have two more international windows that they could play in next year, in March and early June, before the world cup kicks off on June 11.
