Super Eagles home based team lost 4-5 on penalties against the Black Galaxies of Ghana.
Nigeria home based national team came back from a disappointing two goals deficit at the first leg to win 2-0 in Abuja and push the game to penalties but lost 4-5 in the shootout.
Daniel Afriyie and Seidu Suraj gave the Black Galaxies a first leg advantage against the Super Eagles.
However, the CHAN Eagles scored two second half goals in the second leg of the tie played at a scanty 60,000 MKO Abiola stadium in Abuja.
Zulkifilu Muhammed broke the deadlock for the second leg in the 74th minute, giving Nigeria a fighting chance as the match got closer to the end.
Nigeria successfully drew level with a goal in additional time from Chijioke Akuneto to drag the tie to penalties.
Black Galaxies of Ghana eventually won the penalty 4-5 after one of the Super Eagles star missed from the spot.
The Black Galaxies would represent West Africa at the 2023 CHAN scheduled to take place in Algeria.