The South Americans have not won a qualifying game since November 2016 and currently sit eighth in CONMEBOL standings with two rounds remaining.
While the top four teams directly qualify for the World Cup, the fifth-placed side can make it to Russia if they win a home-and-away playoff against New Zealand.
Replacing Quinteros at the helm is 53-year-old Argentine, Jorge Celico, who will take over on an interim basis, according to a satement released by the Ecuadorian Football Federation on Thursday (AEST).
Celico's first responsibility will be to prepare the team for the final two qualifiers against Chile in Santiago and Argentina at home in Quito next month.
Ecuador can still qualify for next year's tournament in Russia if they win both matches and other results go their way.