Elsewhere, surprise early leaders Toulouse maintained their 100 percent start to the season by edging past promoted Arles-Avignon 2-1.
Olympique Lyon scored their first league win of the campaign at the third attempt, defeating promoted Stade Brest 1-0 courtesy of a first-half goal by Cameroon midfielder Jean Makoun.
Argentina defender Gabriel Heinze put hosts Marseille in front from close range early on and Nigeria defender Taye Taiwo doubled the advantage after the break with a low angled drive from just outside the box.
Roars of appreciation from the Velodrome stands greeted Marseille's much-needed victory. It came after they started the season with two successive defeats and the news that new signing from Nice, Loic Remy, had been diagnosed with a heart problem.
"This first win took a long time to come," goalkeeper Steve Mandanda told reporters.
"We needed it because things were getting really complicated," added Marseille's new captain. "Now we must not get carried away. We still have plenty of work to do."
Remy, who awaits tests on Monday to find out how serious his heart defect is, watched from the stands as did fellow France striker Andre-Pierre Gignac.
Marseille have reached a deal with Toulouse for Gignac's transfer and the player is expected to sign a five-year contract this weekend.
"It's not easy to concentrate on football with all the things that have been happening," said Marseille coach Didier Deschamps. "We're all hoping Loic Remy will be playing for us soon."
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