The Manchester United winger was sent off for the second time in four international fixtures as Les Bleus finished top of the group ahead of Switzerland
The fate of Reinaldo Rueda's men was always likely to be partly governed by Switzerland's result against Honduras - with a 3-0 Swiss win in Manaus helping to end Ecuador's hopes.
But an inability to take the chances they created against a much-changed France side, as well as Antonio Valencia's second-half dismissal, was ultimately the South Americans' undoing. France too will recognize the need for improvement ahead of a last-16 clash against Nigeria.
France coach Didier Deschamps made a raft of changes, with Les Bleus already virtually guaranteed top spot, as the likes of Morgan Schneiderlin, Lucas Digne and Antoine Griezmann all started.
It led to a disjointed performance in certain parts, but Ecuador was unable to find the goal and the win it was always likely to need.
Ecuador's chances were dealt a blow when captain Valencia was sent off for raking his studs down Digne's knee. That allowed France to see out the game in relative comfort - continuing to rest players ahead of its next test.
France began with purpose as it pressed and harried Ecuador but it was given an early scare when Jefferson Montero got on the end of Valencia's long ball before being crowded out. The lively Griezmann then pulled an effort wide after 10 minutes as France struggled to convert its possession into clear-cut chances.
If France was frustrated in possession early on, it was put under increasing pressure after the half-hour mark.
Exhibiting tidy passing and smart movement, Ecuador caused France problems without forging any goalscoring opportunities.
Paul Pogba and Valencia both had headers saved by their opposing goalkeepers late in the half but neither side could break the deadlock before the interval.
Griezmann's flick was tipped onto the inside of the post by Dominguez shortly after the break before Ecuador captain Valencia was dismissed for the second time in his last four international appearances.
Rueda was then left to rue Cristhian Noboa's wayward finishing after Valencia had robbed Pogba of possession.
However, if France was troubled by an Ecuador side with 11 men, it could afford to coast somewhat following the dismissal of Ecuador's captain - Pogba almost making life more comfortable when he went close with a header late on.
Dominguez capped off a fine performance for the South Americans with smart saves to deny Benzema and Loic Remy in the final minutes, but it was not enough to stop them from heading home early.
It proved far from vintage for Deschamps' men but an unbeaten group stage still represents progress for Les Blues after their shambolic exit in South Africa four years ago.