The defeat means Usuthu remain third in Group B, level on six points with ES Setif, but the Algerians have two matches left to play while the KwaZulu-Natal-based side only have one game remaining.
In contrast, Raja Casablanca have now qualified for the knockout stages having won four of their five group matches in the continental tournament to sit on 12 points.
Raja Casablanca showed their pedigree on Friday, scoring an early goal through Hamid Ahadad in the sixth minute and then implementing a tactical masterclass to see out the game, adding a second strike through Ilias Haddad late on.
The visitors started the match fast and took the lead when Ahadad latched onto a long ball over the AmaZulu defence and the forward showed his composure to lob goalkeeper Veli Mothwa.
AmaZulu will travel to Guinea for their final match
The match-sealing goal came in the 76th minute when Haddad lashed the ball past Mothwa after the home side failed to clear their lines from a corner.
AmaZulu’s final game in the group will be away in Guinea against Horoya AC on Friday, 1 April.