Having won the first leg away from home a fortnight ago, many had expected the Flying Eagles to seal their place in Zambia in an emphatic style in Lagos.
However that was not the case as a more purposeful display by the Sudanese saw them snatch the ticket via the away goals rule as aggregate scores stood at 5-5.
This is a new low for Nigeria whose national team have failed to qualify for the last two Afcon finals.
The 2017 Africa U-20 Cup of Nations will be the 20th edition of the biennial international youth football tournament organized by the Confederation of African Football (CAF) for players aged 20 and below.