Benin booked their spot in the final round of qualifying after beating 7-6 in a penalty shoot-out in Cotonou.
The second leg at the Stade de l’Amitie ended 1-1 with both sides tied 2-2 on aggregate.
The first leg between Nigeria and Benin comes up on August 11 in Cotonou.
The home eagles camp opens today in Kano.
Coach Yusuf is optimistic Nigeria will advance to the 2018 CHAN tournament in Kenya.