The Peoples Elephant were bundled out of the competition 4-0 on aggregate.
Enyimba were hoping to cancel out the 1-0 deficit from the first leg but found their hosts too strong on the night.
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Ayoub El Amloud gave Wydad the lead on four minutes after he was set up by Yahya Jabrane.
The home team doubled their advantage six minutes before break the through Jamal Harkass.
Yahya Attiyat-Allah netted the third in the 44th minute.
Wydad will face Esperance of Tunisia in the semi-final.
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