Leading 1-0 in the second leg at home in Rades, ES Tunis claimed a 2-1 aggregate win in a game which saw play stopped not long after the hour-mark.
Youcef Belaili had scored the only goal of the game in the 41st minute before the chaotic scenes after the break.
Walid El Karti appeared to head in an equaliser for Wydad Casablanca in the 59th minute, but it was wrongly ruled out for offside.
But a reported VAR (video assistant referee) technical fault meant the decision could not be overturned, leading to protests from the Moroccan side.
After arguments on the sideline, the game was stopped for more than an hour as the teams stood around and waited.
Eventually, the referee whistled for full-time, handing ES Tunis its fourth title and sparking wild celebrations.