El Morabity finished first ahead of his compatriot Aziz Yachou, while Rachid El Morabity camed third.
In women's category, Spanish Anna Comet finished first with a time of 3h 26min 49sec, ahead of French Sylvaine Cussot (3h 35min 51sec) and Moroccan Aziza El Amrany (3h 49min 11sec).
The 4th stage will connect El Mahrach to Jebel Mraïer in the province of Errachidia on Wednesday over a distance of 85.8 km.