Local newspaper Ouest France reported clashes between fans prior to the game, which was then interrupted for a few minutes because of lit flares.
Marseille prevailed through goals by Germain, Morgan Sanson and Florian Thauvin, exposing the home defence's weaknesses.
The Provence side are fourth with 41 points from 20 matches, one point behind second-placed Monaco, who were held to a goalless stalemate at Montpellier, the league's best defence, also on Saturday.
Third-placed Olympique Lyonnais, who are level on point with Marseille, take on Angers on Sunday while runaway leaders Paris St Germain, on 50 points, will travel to Nantes without the injured Neymar.
At the Roazhon Park, Thauvin saw his penalty kick in the 28th minute saved by Tomas Koubek, but Marseille were soon rewarded for their early domination.
In the 35th minute, Thauvin's through ball was collected in the box by Germain, who coolly slotted it past Koubek to open the scoring.
Sanson doubled the tally on the stroke of halftime with a fine half-volley on the turn from Germain's perfect cross.
Thauvin wrapped it up seven minutes from time as he headed home from Luiz Gustavo's teasing cross from the left.
Nice are sixth on 30 points after beating Amiens 1-0 at home.
(Reporting by Julien Pretot; Editing by Christian Radnedge)
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