The U.S., who gave Klinsmann his first win as coach with a 1-0 victory over Honduras at the weekend, slumped to their third loss in five games under the German's attack-minded direction after Jaime Ayovi headed in a cross from team mate Walter Ayovi in the 79th minute.
Klinsmann pledged to turn the U.S. into a more offence-driven side after taking over from Bob Bradley in July, but the transition is yet to show on the scoreboard, with only two goals produced from the last five games.
Still, Klinsmann was encouraged by what he saw on Tuesday, particularly in a first half that featured a number of promising forays before Ecuador lifted after the break.
"In the first half we controlled the match completely," Klinsmann told reporters. "In the second half it opened up because we made a lot of changes - it was our second game in three days.
"A team like Ecuador was a good benchmark. If you make one little mistake they punish you, and that's what they did."
Klinsmann made a number of subsitutions in the second half and pacy Ecuador quickly assumed control of the match.
The breakthrough came when Jaime Ayovi slipped in front of American defender Tim Ream in the box and headed a cross past goalkeeper Tim Howard.
It was Ayovi's second goal in as many matches after he scored in Ecuador's 2-0 win over Venezuela on Friday.
The U.S. received another solid performance from 22-year-old Danny Williams in just his second cap, along with Brek Shea and defender Oguchi Onyewu.
The Americans were without playmaker Landon Donovan, who was sidelined with a quadriceps injury. Like Klinsmann, the veteran international also came away optimistic about the new-look U.S. side's prospects.
"I thought we played pretty well for long stretches, just like in the Honduras match," Donovan said. "So many of these games come down to one play, and that's what you saw."
