Sixteen candidates are vying to succeed President Lenín Moreno, a protege-turned-rival of former President Rafael Correa, who governed Ecuador for a decade and remains a major force.
Colombia managed to score from the spot with James Rodríguez at the end of the first half, giving some hope to the visitors.
The hosts predictably dominated possession but struggled to break down an organized and physical Ecuador outfit that proved a different proposition to the one dispatched 6-1 in a friendly a year ago.
Messi single-handedly rescued Argentina's World Cup hopes as the South American giants came from behind to win in Quito.
With more than 94 percent of voting acts counted Moreno won 51 percent of the votes to 49 percent for conservative banker Guillermo Lasso.