Marseille have struggled by their standards for much of the Ligue 1 campaign, but kept themselves in contention for a place in the UEFA Europa League with the hard-earned victory.
Former Athletic Bilbao boss Marcelo Bielsa was in the stands at the Stade de la Mosson as reported negotiations over a deal for him to take over at Marseille continue.
And he will have been impressed by Marseille's resolve after the Provencal club overcame a spirited Montpellier side to claim triumph.
Marseille took the lead in the 42nd minute, attacking midfielder Mathieu Valbuena scoring with an improvised lofted volley that looped over Montpellier goalkeeper Geoffrey Jourdren and into the net.
However, Montpellier responded three minutes into the second half as M'Baye Niang saw a shot saved by Marseille keeper Steve Mandanda, only for playmaker Remy Cabella to slot home the rebound.
Andre-Pierre Gignac restored Marseille's advantage just before the hour mark, the France international converting Brice Dja Djedje's right-wing cross to net his 20th goal of the season.
But again the visitors could not preserve their lead, and Montpellier levelled for a second time 11 minutes from the end through Morgan Sanson.
The midfielder tapped in after Cabella had tricked his way into the box and forced Mandanda into a fine stop.
Yet there was to be a final twist in the tale in the 89th minute when Payet's long-range drive deflected past a stranded Jourdren.
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