The wine "Bicicleta" from Chile's Cono Sur is the wine in question, and will only be allowed on the promotional events outside France, in Switzerland, Andorra and Spain.
But domestic wine producers were up in arms.
"It's unacceptable to allow the Tour de France organizers to promote a wine from Chile," the Young Farmers group (JA) said on its website. "They should be supporting only French produce."
"How did it come to this surprising end?" asked Socialist Party senator Roland Courteau in a letter to Tour director Christian Prudhomme.
The group had threatened to disrupt one of the stages in the Aude region between Carcassonne and Montpellier if the partnership goes ahead, however Tour de France organizers have made an attempt to appease local wine producers by inviting them to showcase their products during the race.
Race supremo Christian Prudhomme told AFP on Thursday that he and five-time Tour winner Bernard Hinault met the producers for talks at the annual Paris Agriculture Fair this week.
"We discussed the idea of regional producers showcasing their products at all the towns on the Tour itinerary," Prudhomme said.
The head of the French wine producers council Jerome Despey of FranceAgriMer, who invited Prudhomme to the Agriculture Fair, said the matter was settled, adding: "It would have been a mistake to block the Tour de France." said Despey. "
The company that runs the Tour, ASO, has so far insisted it sees nothing wrong with the deal.
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The Tour de France runs from July 2nd-24th.