It marked the third time in five games the American team had been shutout under new head coach Jurgen Klinsmann, who took over from Bob Bradley in July.
Walter Ayovi set up the goal with a cross pass from the left side, that Jaime Ayovi headed past US goalkeeper Tim Howard from the middle of the penalty area.
Ecuador opened their 2014 FIFA World Cup™ qualifying campaign on Friday with a 2-0 home victory over Venezuela with Ayovi again the sole goalscorer. He entered Tuesday's friendly as a second-half substitute.
Jozy Altidore spurned one of the USA's best opportunities to score in the opening minute of the game.
The US beat Honduras 1-0 for the first win under Klinsmann on Saturday.
"It's going to take time," Howard said of the start made under Klinsmann. "People are going to ask questions, and that's natural. But it's still in the infant stages."
Once again the US must have felt like they were playing on the road instead of at home as the crowd of 20,707 was decidedly pro-Ecuador.
The Americans are now winless in their last 13 games against South American teams, dating back to a win over Ecuador four years ago.
Since drawing with Mexico, the Stars and Stripes have lost to Costa Rica, Belgium, and Ecuador under the reign of former German national team star Klinsmann.