The result lifted Ecuador to third in the South American group, equal on points with Chile but with a superior goal difference and three ahead of 2010 semi-finalists Uruguay.
With Argentina and Colombia having qualified, the other three teams are vying for the two remaining automatic tickets to Brazil with the team finishing fifth after Tuesday's final round qualifying for a playoff against Jordan for one more berth.
Ecuador are looking to reach their third finals in four World Cups in Brazil next year after missing out in 2010.
Montero ghosted in behind Maxi Pereira to steer the ball home from less than two metres as goalkeeper Fernando Muslera failed to cut out Antonio Valencia's low cross on the half hour.
The goal brought Uruguay out of their shell trying to manage their energy in the thin air at the Atahualpa in Quito, 2,800 metres above sea level.
The rest of the match went from end to end with chances for both teams and Ecuador goalkeeper Alexander Dominguez had trouble pushing out striker Luis Suarez's dipping free kick in first half added time.
The home side appeared to have scored a perfectly valid second goal 15 minutes from time that would have secured their victory before a nervy final quarter of an hour.
However, the linesman ruled striker Joao Rojas was offside though television replays showed the player was well onside when the ball was passed to him on the edge of the box.
Uruguay need a high-scoring win over Argentina in Montevideo on Tuesday to have a chance at the automatic qualifying berth and sending Ecuador or Chile, who meet in Santiago, to the playoff next month.