After being knocked out of the Coupe de France on penalties by fourth-tier Grenoble last weekend, the Ligue 1 leaders were looking to pile the pressure on their nearest challengers with victory at the Stade de la Mosson on Friday.
But Marcelo Bielsa's men produced another disappointing performance, which leaves both Lyon and PSG with the chance to overhaul them with wins over Toulouse and Bastia respectively.
The contest was preceded by a minute's silence in honour of the victims of the Charlie Hebdo shootings in Paris on Wednesday.
Montpellier opened the scoring nine minutes before half-time through former Evian striker Kevin Berigaud.
Berigaud collected Paul Lasne's low ball from the right on the edge of the area and hit a fantastic right-footed finish past Steve Mandanda.
Midfielder Lasne then turned goalscorer in the 62nd minute, slotting home from close range after Anthony Mounier had worked his way into the box and squared the ball for the ex-Ajaccio man.
Billel Omrani got Marseille back in the game six minutes later, though, by turning home Brice Dja Djedje's far-post cross.
But the hosts held on to complete the double over Marseille and move up to eighth.
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