Walid El Karty nodded the lone goal on 69 minutes to give the home team a 2-1 aggregate triumph after they forced a 1-1 draw in Egyptian coastal city Alexandria last weekend.
Achraf Bencharki, who equalised in the first leg, set up the goal with a deflected cross for El Karty to score his third goal of the competition.
Victory bridged a 25-year gap for Wydad, who conquered Africa for the first time in 1992 when they defeated Al Hilal of Sudan in the African Cup of Champions Clubs.
The name of the premier African club competition changed to the CAF Champions League in 1997 when a new format and prize money were introduced.
Wydad pocketed a record $2.5 million (about 2.1 million euros) and are guaranteed at least another $1 million by competing at the FIFA Club World Cup in the United Arab Emirates during December.
Although Ahly dominated possession and territory during the goalless opening half, Wydad came closest to breaking the deadlock with 30 minutes gone.
A long clearance from goalkeeper Zouheir Laaroubi set in motion a move that ended with a deflected shot from Abdeladim Khadrouf rattling the crossbar.
Relieved Ahly had a great chance to take the lead four minutes later when first-leg scorer Moamen Zakaria broke clear to go one-on-one with Laaroubi.
But the Egyptian failed to lift his shot sufficiently at Stade Mohammed V and the Moroccan shot-stopper used both hands to make a brilliant block.
Smoke from flares enveloped the pitch as the second half started in the Moroccan commercial capital, making visibility temporarily difficult for the near-capacity crowd.
Wydad were more adventurous as the half progressed, using the flanks to put pressure on Ahly, and forcing their first corner with 58 minutes gone.
Morocco-born Walid Azaro, battling the make an impact as the lone Ahly striker, was withdrawn on the hour by coach Hossam El Badry with Ahmed Hamoudi taking his place.
As the second leg drifted into the final quarter, play continued to be confined mainly to midfield with Wydad in pole position thanks to the away goal.
With 69 minutes gone the deadlock finally ended as El Karty struck with his point-blank header evading Ahly captain and goalkeeper Sherif Ekramy.
El Badry reacted to his team falling behind by introducing veteran striker Emad Meteab and winger Walid Soliman as he sought the goal that would level the final on aggregate.
But it was Wydad who came closest to scoring in a frenetic finish.