The home-based Super Eagles lost via penalties to the Black Galaxies of Ghana in the 2023 Africa Nations Championship (CHAN) second leg qualifier game in Abuja.
The Salisu Yusuf tutored side fell 2-0 in the first leg in Cape Coast, Ghana last weekend.
In the second leg at the Moshood Abiola Stadium, Abuja on Saturday evening, Zulkifilu Muhammed opened the scoring for Nigeria in the 76th minute.
Chuks Akuneto got the second goal for Nigeria in added time to take the game to penalty shootouts.
Black Galaxies netted all five spot kicks while the Eagles converted four of theirs as it ended 5-4.
Nigeria also failed to qualify for the last edition of the competition in Cameroon.