The home side, who had seen another goal disallowed in the eighth minute when Romain Alessandrini was ruled offside, entertained hopes of a win to end their poor run this season until Moukandjo collected a long ball from Francois Bellugou to equalise in the 37th.
Marseille are stuck in 16th place in the 20-team table with nine points from 10 games. Lorient are eighth, with 15 points.
Sunday's match went ahead with an empty South stand at the Velodrome stadium after Marseille were punished for crowd trouble that marred their Ligue 1 game with Olympique Lyonnais last month.
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(Writing by Clare Fallon in London, editing by Alan Baldwin)
