The super eagles booked their ticket before their match day five fixture against Benin republic, which they won by a lone goal, at the Charles de Gaulle stadium in Porto Novo.
Lesotho and Sierra Leone had played a barren draw to share the spoils.
The result meant that the super eagles were guaranteed a second position, if they lose their last two matches.
But that wasn’t the case as Paul Onuachu justified his inclusion in the squad with a sublime finish in injury time to give Nigeria maximum points.
The win secures top spot for the super eagles in group l, going into the last round of matches in the qualification campaign.
The super eagles will return to Lagos where they will face Lesotho in a mere formality encounter, on match day 6 on Tuesday, at the Teslim balogun stadium.
The last time the super eagles played a competitive match in Lagos was 20 years ago, when they defeated Sierra Leone, in a world cup qualifier.
15 other nations including six former champions apart from the hosts, Cameroon, have qualified for the apex football tournament in Africa, including the most successful Egypt, Ghana, Tunisia, Algeria and morocco.
Comoros Island and the Gambia will make their first appearance at the Africa soccer fiesta.