The court in the central city of Orleans dismissed the charges of organised vandalism against the 49, who had uprooted GM maize in the region planted by Monsanto, the American biotechnology group, in two incidents, one last year and the other this year.
"The defendants have shown proof that they committed an infraction of voluntary vandalism in a group to respond to a situation of necessity," the court said.
That situation of necessity "resulted from the unbridled distribution of modified genes that constitutes a clear and present danger for the well-being of others, in the sense that it could be the source of contamination and unwanted pollution", it said.
The court, however, upheld a civil complaint against the defendants, ordering them to pay $7,000 to Monsanto in damages and interest. Monsanto had been seeking more than $300,000.
Jean-Emile Sanchez, one of the activists, called the verdict "a huge victory for the anti-GM side" and said the judgment would form an important legal precedent.
Alex Perrin, the state prosecutor in the case who had pressed for jail terms for all of the defendants, and Monsanto said that they would appeal against the decision.
The defendants had included two Green Party politicians, one of whom, Yves Contassot, is a deputy mayor of Paris in charge of environmental issues.