Reinaldo Rueda's men could have put breathing spaces between themselves and fifth-placed Uruguay ahead of their match against Colombia on Tuesday.
But the hosts, bottom of the group, doggedly ground out a point after substitute Jaime Arrascaita's goal had threatened to hand them a rare win.
Felipe Caicedo's penalty earned the visitors a draw but they will see it as two points dropped.
Rueda made five to the side that lost 1-0 to Colombia, one was enforced as Gabriel Achilier was suspended for the clash.
Bolivia brought in several new faces, too, including goalkeeper Romel Quinonez, who replaced Sergio Galarza following his error-ridden performance in the 4-0 loss to Paraguay.
Bolivia found their feet as the half went on and managed to hold onto the ball for longer periods than in the opening quarter.
Juan Arce dragged a shot just wide of Alexander Dominguez's goal just after the half-hour mark to underline their growing threat.
Bolivia got another sight of goal right on half-time. Alejandro Chumacero got behind the Ecuador defence and was about to shoot when Juan Carlos Paredes intervened with a strong challenge.
The second half saw Bolivia take a surprise lead and it was introduction of Arrascaita that made the difference.
But they were made to rue the two missed opportunities three minutes later when Ronald Raldes Balcazar tangled with Montero in the area, handing the visitors a penalty.
