The host were outplayed by the visitors, crowned Moroccan league champions few months ago, and were by far the better side of the closely contested encounter in Marrakech.
A game of few chances in the opening minutes, it was the 2010 champions who broke the deadlock from the spot after Abdelilah Amini handled from a free-kick just outside the penalty area on 23 minutes.
Forward Youssef El Gnaoui elected himself for the kick and sent Kawkab goalie Mohamed Ozouka, who has featured in all his side’s 10 matches so far this season, the wrong way for the opener.
Kawkab replied in stoppage time of the first half also from a penalty with Si Mohamed El Fakih converting with ease.
The second half belonged to FUS Rabat who took their chances and restored their lead barely two minutes after the break through captain Abdessalam Benjelloun, formerly on the books of Scottish top flight side, Hibernian and Belgian outfit, Chaleroi.
Strike partner Adam Ennaffati halted an attack by Kawkab, beating his marker before laying to Benjelloun, who fired a low shot past Ozouka.
The visitors took the game beyond their hosts with the third goal on 67 minutes from Mohammed Fouzair with a grounder that deflected off Malian-import Boubakar ‘Kiki’ Kouyate past a hapless Ozouka.
FUS will host Kawkab in the reverse on Wednesday, 27 July 2016 in Rabat and will be hoping to complete a double over their fellows to inch closer to the last four.
Meanwhile, holders Etoile du Sahel will host Libyan side Ahly Tripoli in other Group B Day 3 fixture on Saturday, 16 July 2016 in the Tunisian Mediterranean resort city of Sousse. Etoile has just a point from their previous two games whilst Ahly Tripoli are pointless.
16.07.2016 Young Africans (Tanzania) vs Medeama (Ghana)
17.07.2016 MO Bejaia (Algeria) vs TP Mazembe (DR Congo)
15.07.2016 Kawkab (Morocco) 1-3 FUS Rabat (Morocco)
16.07.2016 Etoile du Sahel (Tunisia) vs Ahly Tripoli (Libya)