Edafe Egbedi scored the second-half winner as Nigeria edged England 1-0 to reach the quarter-finals of the Under-20 World Cup in Colombia.
Nigeria, who reached the final in 1989 and 2005, play France next on Sunday.
"It was a difficult match but we were the ones who took more risks," said Nigeria coach John Obuh.
Striker Matthew Phillips had two chances late on to equalise for England, but he fired over the crossbar both times.
Obuh, who was wearing a Colombian sombrero and earned the support of the local fans, added that he felt the English played very defensively.
The Nigerians, who have won all four of their matches, had a few chances to extend the lead with long-range shots near the end, but England goalkeeper Jack Butland came up with difficult saves to keep his team in the game until full time.
More than 30 eligible English players were not released by their clubs for the tournament.
"If you look at the results, you can say it was a failure," England coach Brian Eastick said.
"The only way to change that is to change regulations to make the clubs release their players."