Hamza Lahmar broke the deadlock in Marrakech by converting a 61st-minute penalty for Etoile, the only club to win all five past and current CAF competitions.
Kawkab, first time qualifiers for the eight-club mini-league phase of the second-tier African competition, responded by laying siege to the Etoile goalmouth.
Boubakar Kouyate levelled on 74 minutes and Abdelilah Amimi grabbed the winner four minutes from time.
Morocco are the only country with two representatives and 2010 Confederation Cup winners FUS Rabat host Al Ahly Tripoli of Libya Sunday in the other Group B fixture.
In Group A, TP Mazembe of the Democratic Republic of Congo host Medeama of Ghana and Mouloudia Bejaia of Algeria have home advantage over Young Africans of Tanzania Sunday.