The Eagles beat Sudan 1-0 on Wednesday through a lone goal from Gabriel Okechukwu while Morocco beat Libya 3-1 after extra time in the semi-finals to book a final clash with the Eagles.
Morocco coach Jamal Sellami paid tribute to his team after their victory, which was inspired by a brace from striker Ayoub El Kaabi.
Zakaria Hadraf put Morocco ahead in the 45th minute. El Kaabi converted from a corner kick but his effort was ruled out for a goal kick by referee Bakary Gassama for an infringement.
The North African country is also the first nation to host and win the tournament reserved for players playing in their home countries.
The Atlas Lions made the numerical advantage count in the 61st minute when Walid El Karti headed home the rebound after Ajiboye had initially stopped Ismail El Hadad's volley.
The host, Morocco were by far the better side as they tore apart a hapless Nigeria team, who ended the game with a man less after Eneji Moses was given a red card early in the second half.
Nigerian Gabriel, who scored the extra-time victor against Angola in the quarter-finals, finished a route-one move by darting through to fire a low shot past Sudan captain Akram Elhadi.
Hadraf got his second of the night on 64 minutes before Ayoub El Kaabi netted the fourth for Morocco - his 9th in the competition - on 73 minutes.
"It surprised me to see the players survive the remaining minutes of the game against Sudan after been reduced to 10 men with Ifeanyi ifeanyi sent off in the 59th minute".
The hosts are packed with pace and power and will be hoping to entertain their fans when they face the Super Eagles in the finals.
Meanwhile, Sudan overcame Libya on Saturday to take third place.