The Eaglets were beaten 2-1 by Burkina Faso in a quarter-final clash in Algiers on Thursday night.
The result means the Eaglets will not be at this year’s FIFA U-17 World Cup billed to hold from 10 November to 2 December 2023 in a yet to be decided country.
Burkina Faso complete Africa’s representatives at the World Cup after Senegal, Mali and Morocco booked their tickets earlier by reaching the AFCON semifinals.
Burkina Faso went 1-0 up in the 44th minute through Aboubakar Camara who scored following a poor clearance by Tochukwu Ogboji.
Camara went on to double the lead of the Burkinabes when he converted from the penalty spot in the 56th minute.
Abubakar Abdullahi then pulled a goal back for the Eaglets in the 68th minute which turned out to be a consolation strike as Burkina Faso held on to advance.
Nigeria had started the competition with a 1-0 victory over Zambia, losing 1-0 to Morocco in their second game before emerging winners of a five-goal thriller against South Africa in their final group game.