Renaissance Berkane won the second-tier CAF Confederation Cup on May 20 and will face Wydad for the CAF Super Cup.
Wydad coach Walid Regragui promoted El Moutaraji from the bench for the title decider and it proved a masterstroke as he netted after 15 and 48 minutes in Casablanca.
It was the third time Wydad have conquered Africa, winning in 1992 and 2017, and the second triumph also came against Ahly.
Ahly, seeking a record third straight title, had plenty of possession but were undone by the clinical finishing of the Moroccans.
It was also a disappointing outcome for South Africa-born Ahly coach Pitso Mosimane, who had hoped to become the first coach to win the premier African club competition three consecutive times.
Both Wydad and Ahly showed one change to the sides that drew semi-final second legs against Petro Luanda of Angola and Entente Setif of Algeria respectively to reach the final.
France-born Regragui preferred El Moutaraji to Badie Aouk in midfield, with the latter among the nine substitutes.
A groin injury ruled out Ahly centre-back Mohamed Abdelmonem and Mosimane promoted another Egyptian international, experienced Ayman Ashraf.
Close to 40,000 singing, dancing, cheering, flag-waving Wydad supporters greeted the teams as they entered the pitch, with FIFA president Gianni Infantino among those looking on.
Ahly were allocated 10,000 tickets, but only a couple of thousand supporters flew across the north of the continent to attend the highlight of the African club season.
– Controversial venue –
The Stade Mohammed V — home ground of Wydad — was a controversial choice of venue with Ahly making a failed appeal to the Court of Arbitration for Sport (CAS) to have it changed to a neutral one.
Morocco were the lone bidders to host the final after Senegal withdrew, and the Confederation of African Football (CAF) said the rules did not permit a change.
Wydad attacked from the kick-off and after rattling the woodwork, went ahead in the 15th minute as El Moutaraji justified his promotion.
Earlier, Congo Brazzaville-born Guy Mbenza was foiled by the crossbar after his shot from just outside the box beat Ahly captain and goalkeeper Mohamed el Shenawy.
But the Moroccans went ahead four minutes later as El Moutaraji unleashed a swerving thunderbolt from outside the penalty area which flew over El Shenawy and into the net.
Ahly clawed their way back into the match and came close to levelling midway through the half when a Yasser Ibrahim header off a corner was just too high.
Ahly were dangerous from set pieces and Hussein el Shahat nodded narrowly wide off another corner for the Cairo Red Devils.
The visitors came close again with Wydad goalkeeper Ahmed Tagnaouti dashing from his goalmouth to head the ball clear as South African Percy Tau threatened to equalises level.
Wydad doubled the lead three minutes into the second half and once again El Moutaraji was the executioner.
His first attempt from close range was parried by El Shenawy, but the Moroccan reacted quickest to push the rebound into the net.
Mosimane rang the changes as the second half progressed, including introducing leading scorer Mohamed Sherif, but the Cairo club could not find a way through the Wydad defence.
Sherif came tantalisingly close to adding to his six Champions League goals this season with eight minutes remaining, but Tagnaouti parried his close-range poke and the ball was cleared.