Mike Serumagga scored the lone goal after 46 minutes to hand the Cranes a morale boosting win, after the events of October 2011, where they just fell short of qualifying for the 2012 AFCON championships.
The Moroccans, totally dominated the game afterwards, but lack of cutting edge and a solid rearguard display from the Ugandan's preserved their lead.
Coach Bobby Williamson, watching from the sidelines was ecstatic at the final whistle, content with a hard fought win, against a high quality side.
Sudan will be next up for the Cranes, on Sunday 13 November 2011, for whom Sofapaka midfielder Mussa Mudde travelled with to the North African country.
It will be a battle of East African teams in the match, which Sudan will work hard in after going down 3-1 to Cameroon, earlier on, in their opening match of the tournament.