It gave them a 3-2 aggregate win in the first edition of Africa’s effort at launching a super league, which was reduced from a planned 24-club league to a six-week, eight-team knockout tournament.
Trailing 2-1 from last weekend's first leg in Casablanca, Sundowns evened the aggregate score in stoppage time at the end of the first half through Peter Shalulile.
They added a second goal seven minutes into the second half when Aubrey Modhiba stole away possession before chipping the ball over the Wydad goalkeeper.
A super league for Africa was originally suggested by FIFA president Gianni Infantino, who condemned similar efforts in Europe while saying it could transform the game in Africa.
He attended the match in Pretoria on Sunday, along with a capacity crowd who had been granted free entry.
