Quinteros, 49, is a former international for Bolivia, who he also coached from late 2010 until mid-2012.
He will coach Ecuador for their upcoming Copa America campaign and lead them in 2018 World Cup qualifying.
"It comes at the best moment of my career, because one gains experience as you work in this profession," Quinteros said.
"I am eager and full of dreams, and hopefully form a team that plays good football and brings joy to people."
Sixto Vizuete was at the helm on an interim basis after Reinaldo Rueda's contract was not renewed following Brazil 2014.
Ecuador will face Chile, Mexico and Bolivia at the Copa America, which begins on June 11.
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