With just 12 minutes on the clock, captain Ghizlane Chebbak opened the scoring with a brilliant strike from outside the box, curling the ball low past Nigerian goalkeeper Chiamaka Nnadozie.
A slick pass from Ibtissam Jraidi found Mssoudy in space, and the forward made no mistake with a composed finish into the bottom right corner.
Nigeria appeared stunned and went into the break trailing by two goals.
The comeback began just after the hour mark when a VAR review handed Nigeria a lifeline.
A handball by Nouhaila Benzina resulted in a penalty, which was coolly dispatched by Esther Okoronkwo to make it 2-1.
From that moment, the momentum swung Nigeria’s way.
In the 71st minute, Okoronkwo turned provider, slipping a neat ball into the path of Folashade Ijamulusi, who drilled a left-footed effort into the bottom corner to bring Nigeria level.
With the match heading towards extra time, Nigeria found the winner.
A well-worked set-piece situation saw Okoronkwo once again involved, delivering a clever assist to Joe Echegini, who calmly slotted home in the 88th minute to seal a dramatic turnaround.
In spite of the late pressure, the Super Falcons held firm through a tense final few minutes of stoppage time, to clinch a 10th title in 13 editions of the tournament.
Nigeria’s Nnadozie and captain Rasheedat Ajibade were named Goalkeeper and Player of the tournament respectively.
The Super Falcons had dispatched the defending Champions South Africa 2-1 in the semi-final.
