Esperance almost succumbed to an early lead by Raja, but a shot from Soufiane Rahimi failed to beat Rami Jridi who saved easily inside the opening 10 minutes.
Twelve minutes later, Jridi was beaten hands down when a combination of passes set up Abdelilah Hafidi who found the bottom corner.
The Tunisians' best chance arrived near the latter stages when Yassine Khenissi draw a close-range save from Anas Zniti on 37 minutes.
Right from the restart, Esperance changed their attacking formation with Youcef Belaili replacing Saad Bguir.
The move moved paid off in the 57th minute as Belaili found the top corner with a sumptuous finish following an exciting move.
The Green Eagles regained control after Badar Banoun flicked home a goal-bound shot from a goal-mouth scramble with 25 minutes remaining.
With glaring gaps from Esperance, Jridi blocked a close-range chance from Mahmoud Benhalib in the latter stages of the half.
The Tunisians searched for a way back, but in the end the Moroccans walked away with their second Super Cup title since 2000.