The Flying Eagles played a man short after 63 minutes when defender Ikechukwu Okorie was sent off for dangerous tackle.
“We will do well at the AYC. We are just preparing for the tournament,” assured Nigeria skipper Abduljaleel Ajagun after the game played at the FIFA Goal project in Abuja.
The host team, who played out a 1-1 draw when both teams first clashed in September, started out brightly and created some openings.
Left back Kingley Madu let fly a low pile driver after six minutes and after 27 minutes Umar Aminu’s header from inside the box was saved by the impressive goalkeeper Ariston Hessou.
Madu made another attempt at goal on 34 minutes, before skipper Ajagun missed just before the interval.
Benin’s best chance was three minutes after the break when Nigeria-born striker Ezekiel Okotou forced Flying Eagles goalkeeper Jonah Usman to scramble his goal-bound shot for a corner.
Benin, who paraded as many as six Nigeria-born players, took control the game soon after Okorie was sent off just after Ajagun missed the biggest chance of the game when from inside the box he fired wide in front of an open net a minute earlier.
Despite their numerical disadvantage, Nigeria created the better chances especially in the dying moments of the match.