The News Agency of Nigeria (NAN) reports that Enyimba looked bright and eager at the start in Casablanca, but by the time they let in a soft goal in the first half stoppage time, the fight was all but taken from them.
A blunder by defender Isiaka Oladuntoye gifted Raja in the dying moments of the first half, while Oladuntoye then put the ball into his own net late in the second half.
However, substitute Abdulrahman Bashir scored a late consolation goal for the Aba Elephants.
The Moroccans will face AS Vita of Congo in the final.
Vita Club also dumped out Al Masry of Egypt after they trounced them 4-0 earlier Wednesday.