The Golden Eagles hopes of yet another Under-17 World Cup football title was stopped in its tracks by a resurgent Netherlands in the last 16.
Nigeria, five -time champions at the junior level, were beaten 1-3 by the Dutch side, who had only barely qualified for the knockout stages.
The Dutch had lost their first two matches of the competition and only got into the knockout stage thanks to their 4-0 defeat of USA in their final group phase encounter.
Nigeria, despite a shock defeat to Australia had topped their group with wins over Hungary and Ecuador, and were looking to book their place in the quarter-finals in the match played in Goiania, Brazil.
However, the form books were turned upside down with Sontje Hansen opening score for the Netherlands in the fourth minute.
Nigeria drew level with a blistering shot from Olakunle Olusegun in the 12th minute only to see Hansen pick up his second three minutes later. Poor defending of a free kick in the 15th minute gifted Hansen an easy chance to put his side ahead once again with a drive from the edge of the box that went past a diving goalkeeper Daniel Jinadu.
Hansen got his hattrick off a penalty awarded eleven minutes from time. The Dutch were warded the spot-kick after the Video Assistant Referee (VAR) spotted a handball by Clement Ikenna.
Netherlands will play the winner of the match between Paraguay and Argentina in the quarter-finals.
Also through to the last eight are South Korea. The Koreans, one of the two Asian sides in the last 16, edged Angola 1-0 in their last 16 match, They had progressed to the knockout stages as the runners-up in Group C behind France while Angola had qualified as runners-up from Group A behind hosts Brazil.
In the match, played earlier at the Estadio Olimpico in Goiania, Choi Min-seo found the net in the 33rd minute to earn them a quarter-final spot.
Choi slotted a rebound past Angola goalkeeper Geovani de Carvalho after he had kept out Jeong Sang-bin’s initial attempt.
The Koreans will now face the winners of the match between reigning Asian U16 champions Japan and Mexico in the last eight.
The other last 16 matches to be played over the next few days are Spain vs Senegal, France vs Australia, Equador vs Italy and Brazil vs Chile.