Sfaxien, seeking a treble of Confederation Cup triumphs, were firm favorites to lift the trophy after holding FUS to a goalless draw in Morocco in the first leg.
However, FUS gave them food for thought about their tough mission after grabbing the lead through a header from Abdelfettah Boukhriss as early as the seventh minute.
Sfaxien, needing two goals to avoid a surprise defeat, leveled the score after Hamdi Rouid made the most of Lassad Dridi's free kick on the stroke of halftime.
Sfaxien playmaker Kamel Zaiem put the hosts in front after converting a 49th-minute penalty as the Tunisians looked on course for a likely victory.
But a close-range shot by Mohamed Zouidi in the 75th minute gave FUS the upper hand in terms of the aggregate score.
Sfaxien piled on pressure to notch the winner but FUS exposed their defensive gaps to kill off the game with a cool chip from Zouidi one minute from time.
FUS became the second Moroccan club to win Africa's secondary club competition after city rivals FAR Rabat, who clinched the title in 2005.
They will face Champions League winners TP Mazembe of DR Congo in the African Super Cup.
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