The Kenyan champions were undone after Abderhamane Yusfi bundled home the ball on ten minutes even though it seemed Samuel Onyango had done just about enough to scramble it off the line.
The tap in goal came after reserve keeper Fred Odhiambo had made a double save to keep his team in the match.
Gor were second best in the opening period and the hosts took full advantage, administering several attacks with a view of earning an early advantage.
In the process, Nicholas Kipkurui and Shafique Batambuze were booked earlier on in the game.
Hassan Oktay’s team seemed to have equalised in the second half as Shafik Batambuze ‘sheader off a Francis Kahata corner kick found the net, but the strike was surprisingly disallowed for an infringement.
Following this result, Gor drop to second in their group with six points from four games with NA Hussein Dey leading courtesy of an extra point.
Zamalek are third and Angola’s Petro Atletico are last.