The Provence side, who had never led the standings this season, prevailed thanks to a header by Argentina defender Gabriel Heinze and a penalty from France midfielder Hatem Ben Arfa before the half-hour.
Substitute Bakari Kone added a third in stoppage-time.
Marseille, who were last crowned champions in 1992, lead on 59 points, with a game in hand.
Olympique Lyon are second on 57 points with seven games left, ahead of third-placed Montpellier and Auxerre, in fourth, on goal difference.
Champions Girondins Bordeaux now lie fifth, three points off the pace but with two games in hand while Sochaux are 14th on 37 points.
"Being the leaders tonight is one thing but the most important is to be still the leaders after the last game... There are still lots of points up for grab," Marseille coach Didier Deschamps told reporters.
"We savour the fact we are top of the standings but we must now keep our momentum," he added after Marseille enjoyed their seventh win in their last nine league outings.
Under heavy rain, Heinze opened the scoring for Marseille when he headed home from a corner kick by fellow Argentine Lucho Gonzalez in the ninth minute.
Ben Arfa made it 2-0 from the spot after Marseille defender Laurent Bonnart was downed in the box by Yassin Mikari.
Marseille's only scare came midway through the second half when a deflected shot by Edouard Butin hit the bar.
The home side had the final word though when Ivory Coast forward Kone lobbed goalkeeper Matthieu Dreyer in stoppage time.
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