Sundowns’ defender Mothobi Mvala (28) powered a header into the back of his own net in a botched clearance eight minutes from time to hand Wydad a ticket to next month’s decider against Al Ahly of Egypt.
The first leg of the semi-final in Casablanca ended goalless and the two away goals in the return ensured Wydad’s progress.
Sundowns went ahead early in the second half through captain Themba Zwane (33), stealing the ball away from the Moroccan defence before firing home from the edge of the box.
But Wydad showed their experience to equalise in the 72nd minute with a powerful header from flying full back Ayoub El Amloud (29) from a perfect cross by captain Yahya Jabrane (31).
Sundowns restored their lead seven minutes later through top scorer Peter Shalulile (29) but gave away a second goal three minutes later to end their hopes.
Al Ahly host the first leg of the final on June 4th with Wydad at home in the return a week later as the two clubs reprise last year's decider, which Wydad won 2-0.