Rachid Rokki scored 12 minutes into the second half to settle the north African showdown and lift his team to first place in Group B with six points from three outings.
CS Sfaxien of Tunisia, the only club to successfully defend the second-tier African club competition, slipped to second place two points behind after a 1-0 loss away to Zanaco of Zambia in Lusaka on Saturday.
Another surprise package was not so lucky as Niger armed forces side ASFAN crashed 4-0 to Al Ittihad of Libya in Tripoli with Pan Pierre Koulibaly scoring twice and Sapol Mani and Ahmed Zuway once each.
Al Hilal of Sudan, seeking their first African title after twice finishing CAF Champions League runners-up, are the only contender with maximum points after three rounds having beaten Djoliba of Mali 2-1 on Friday.
But the weekend belonged to FUS, who escaped relegation from the Moroccan Super League only after winning their final game and cannot boast a single big-name footballer. They had to grind through a four-round qualifying competition just to reach the last-eight with their victims including title holders Stade Malien of Mali and three-time South African champions SuperSport United.
And after Zanaco coach Wedson Nyirenda bragged that his club would take the title they came unstuck away to FUS in the opening series of matches four weeks ago. FUS themselves came a cropper in the next round by crumbling at 2007 and 2008 winners Sfaxien only to bounce back against Hodoud, a club based in Mediterranean city Alexandria.
Hodoud must now win a return match against FUS next Sunday to have a realistic chance of a top-two finish and a semi-finals place as they occupy bottom place with two points less than Sfaxien and Zanaco. Koulibaly from Burkina Faso got his brace during the first half, Togolese international Mani claimed the third goal and Libyan Zuway completed the scoring by converting a penalty before the hour mark.
Serb coach Milutin Sredojevic has warned opponents of Hilal that they face "hell" in the searing heat of Omdurman and Djoliba must have feared the worst when Mudather Eltaib and Mohamed Bashir had netted by the 35th minute. But the Bamako-based outfit hoping to become the second successive Malian club to pocket the $660,000 first prize tightened up and Ousmane Cisse pulled a goal back in stoppage time.
Hilal have nine points, Ittihad six and Djoliba and ASFAN one apiece at the halfway stage with the odds favouring the frontrunners despite both being away in two of the remaining three rounds.