Newsonline report that the game ended 2-2 on aggregate after the home Eagles cancelled the Black Galaxies’ first leg advantage.
Zulkifilu Muhammed gave Nigeria the lead in the 76th minute.
With time running out, Chuks Akuneto netted the second goal for the hosts in the last minute of added time.
Ghana scored all five kicks in the penalty shootout, while the home Eagles could only hit the net four times.
Nigeria also failed to qualify for the last edition of the competition in Cameroon.
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