Louis van Gaal's side left it late to win their opener against Senegal and they were similarly unimposing on Friday.
Cody Gakpo's rocket strike on six minutes opened the scoring for Netherlands, but the side were unable to find a second.
Ecuador thought they had equalised on the stroke of half-time when winger Gonzalo Plata's strike from the edge of the box was deflected in, but celebrations were quickly muted when VAR ruled out the goal for offside.
The result leaves Netherlands and Ecuador joint top of Group A on four points, Senegal one point behind in third and hosts Qatar the first team to be eliminated from the tournament.
Ecuador had a subdued first half as van Gaal's side looked comfortable but unhurried. But the South Americans, roared on by a large yellow-clad contingent at the Khalifa International Stadium, stepped up a gear in the second half and could have won it when Plata's strike hit the crossbar.
Plata thrashed a powerful shot onto the woodwork in the 59th minute as the South Americans went from strength to strength, consistently hustling the Dutch off the ball by applying a physically-demanding press that did not allow their opponents to play their usual flowing game.
"They had a few biters, guys who are hot on your heels. Then you have to act quickly, and [we] could have dealt with that better. We should have done better in possession of the ball," Dutch captain Virgil van Dijk said.
It had started out most promising for the Dutch, looking for their second win of the tournament that would have ensured they were the first team to qualify for the knockout stages, when Gakpo scored.
But that was as good as it got for the Dutch side. Valencia's clever pass in the 24th minute sent Caicedo away down the left and, although his touch was heavy and allowed the Dutch to intercept, it provoked a burst of noise from the large number of their fans that injected energy into the Ecuador players.
Valencia cut inside to fire a shot that forced a full stretch save out of Dutch goalkeeper Andries Noppert soon after the half hour mark and, as they kept up the pressure, Ecuador had the ball in the back of the net in first half stoppage time as Pervis Estupinan deflected the ball home.
However, it was ruled out because Jackson Porozo was both offside and standing in front of the goalkeeper and blocking his line of sight.
The equaliser four minutes into the second half was always on the cards, as Ecuador stole possession in midfield and fed Estupinan for a stinging shot on the left that Noppert did well to parry but with Valencia pouncing on the rebound.
The 33-year-old, who went off near the end of the game, has now netted Ecuador's last six World Cup finals goals -- three at the 2014 tournament in Brazil and three in Qatar.