The Falconets were unable to repeat their performance from the previous round of winning all three group stage games in this quarterfinal in Alajuela, Costa Rica.
Flourish Sabastine, who scored Nigeria’s winner against France in the first Group C leg, failed to score after seven minutes.
The Dutch took the lead after four minutes when Zera Hlusuit slammed a perfect drop shot past Omini Oyono after a counterattack.
In the 15th minute, Sabastine had another shot, but goalkeeper Claire Dinkla deflected the ball away.
In the 30th minute, with the Dutch defense in turmoil, Nigeria almost equalized when Deborah Abiodun grabbed the ball, deserving of their effort.
But her takeoff shot from 25 yards smashed the bar and hit Chiamaka Okwuchukwu in the head.
Just three minutes later the Dutch broke through again on the right flank to double their lead.
With captain Oluwatosin Demehin and Omowumi Oshobukola floundering, Ziva Henry shot the ball past Oyono.
In the 62nd minute, substitute Joy Jerry nearly headed in a Rofiat Imran cross, but the ball went wide.
Two minutes into stoppage time, a Dutch defender played the ball inside the penalty area and Nigeria rushed forward.
This defeat comes to the Falconets who had won all three group stage matches, scoring five goals and conceding only one.
The Netherlands will face Spain in the first semi-final on Thursday after the Europeans beat Mexico 1-0 in their first quarter-final on Saturday.
Brazil who also won 1-0 against Colombia on Saturday in the second quarter-final match awaits the winners of the fourth quarter-final match fixture between defending champions Japan and France.