Mokoena equalised in Rabat during first-half added time after Mohamed Hrimat had put FAR ahead from the penalty spot.
But when FAR were awarded a second penalty on 77 minutes, Williams parried the attempt from Hrimat, triggering an exodus from the stadium by thousands of Moroccan supporters.
Both clubs made one change from the first leg with fit Senegalese centre-back Fallou Mendy back for FAR and full-back Divine Lunga replacing the injured Aubrey Modiba for Sundowns.
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Deafening noise greeted the kick-off in front of a near-capacity 60,000 crowd and the Somali referee yellow-carded Moroccan Marouane Louadni and Colombian Brayan Leon within four minutes.
Lunga was then lucky to escape being sanctioned after a late tackle on Hrimat as FAR continually threatened down the flanks.
Hrimat blazed wide after 16 minutes from a pull-back when he should at least have hit the target and the FAR captain then became the third player to be cautioned.
Slick Sundowns passing created a half-chance and Tashreeq Matthews was not far off target with a drive from outside the box.
The second-leg stalemate was broken on 40 minutes when Lunga fouled Reda Slim and Hrimat sent Williams the wrong way from the spot kick to bring the clubs level on aggregate.
Powerful Shot
But after FAR goalkeeper Ahmed Tagnaouti saved a weak close-range stab from Leon, Sundowns drew level on the night seven minutes into added time.
A Leon cross and a Matthews back-heel set up the unmarked Mokoena inside the box and he unleashed a powerful shot that gave the FAR shot-stopper no chance.
With away goals counting double, the Moroccans had to score at least two more goals to become the first champions from Morocco since Wydad Casablanca lifted the trophy in 2022.
The yellow card count rose to six early in the second half with Abdelfettah Hadraf the fourth FAR player into the book and Jayden Adams the second from Sundowns.
FAR’s restless crowd began whistling as their team struggled to create further opportunities.
That frustration increased when Williams atoned for a foul on Youssef El Fahli by parrying the resultant Hrimat penalty at the expense of a corner.
Hrimat opted to place the ball into the right corner, as he did with his successful spot kick in the first half, but Williams stretched out his left arm to push the ball over the crossbar.
Sundowns substitute Lebo Mothiba had the ball in the net during added time, but was ruled offside.
AFP
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