Illias Haddad (8), Fabrice Ngoma (14) and Zakaria Habti (36) had the goals for the Green Eagles who made it five out of five in the group, sitting pretty on top of the log with 15 points.
The visitors took matters easy in the second half with Namungo fighting for pride, but the score didn't change.
Raja will finish top of Group D after the 3-0 whitewash of Namungo FC who will finish bottom of the group.
Last year's losing finalists Pyramids FC squeezed into the quarter-finals of the CAF Confederation Cup after beating Zambia's Nkana 1-0 at the Levy Mwanawasa Stadium in Ndola on Wednesday.
The victory away from home took the Egyptians to second in the Group D standings with nine points, three clear of Nkana with one round of group matches left.