After a 2-2 draw against Burkina Faso in their second Group B game on Wednesday, the Flying Eagles are through to the semifinals with four points from two group games.
As a result of the defeat, the Flying Eagles now have four points, while Ghana and Burkina Faso will compete for the second qualification spot.
The Nigerian team scored through Ibrahim Muhammad and Ibrahim Yahaya.
On Sunday, the Ladan Bosso-led side overcame Ghana’s Black Satellites 2-0 in their group opener.
The Flying Eagles took the lead on 60 minutes of Wednesday’s game, which was played inside Niamey’s Stade Seyni Kountche. Muhammad’s attempted cross from the right sailed into the top corner.
Burkina Faso rallied back to tie the game, but Yahaya converted a penalty in the 69th minute to put the Flying Eagles back in front.
Burkina Faso equalised once more to make it 2-2, but the Flying Eagles held on to advance to the next round.
Daniel Daga of Nigeria was named Man of the Match.
They still need to win their semifinal game in order to qualify for the U20 AFCON.