President Emmanuel Macron posted on X: "Our compatriot Laurent Vinatier is free and back in France. I share the relief felt by his family and loved ones."
He added that he was grateful for work done by French diplomatic officials.
Foreign Minister Jean-Noel Barrot welcomed Vinatier and his parents at the Quai d'Orsay in Paris, the ministry said.
Russia's FSB security service said Vinatier, 49, had been swapped for Daniil Kasatkin, a Russian basketball player who was arrested at a Paris airport last June and who was wanted in the United States for alleged involvement in ransomware attacks.
The FSB said Vinatier had been pardoned by Russian President Vladimir Putin, who promised last month to look into the case after a French journalist raised it during the Kremlin leader's annual news conference.
Vinatier was arrested by the FSB at a Moscow restaurant in June 2024 and convicted four months later of breaking laws requiring individuals deemed to be "foreign agents" to register with the Russian authorities.
While behind bars, he was placed under additional investigation for espionage and he had been facing a likely further trial in coming months.
The FSB statement alleged that Vinatier, acting on instructions from Swiss intelligence, had collected sensitive political and military information - including on combat and training plans - that could have been used to harm Russia's security.
However, it said the case had been dismissed because of his "active repentance".
At the time of his arrest, Vinatier was working for the Centre for Humanitarian Dialogue (HD), a Swiss-based conflict mediation organisation.
Fellow academics said he was a respected scholar involved in legitimate research.
At his trial, Vinatier said he loved Russia, apologised for breaking the law and even recited a verse by Russian poet Alexander Pushkin.
French authorities had maintained Vinatier was arbitrarily detained and had called for his release.
Macron denied that Vinatier worked for the French state and described his arrest as part of a misinformation campaign by Russia.
Kasatkin, the Russian released in France, had denied the US hacking accusations.
His lawyer Frederic Belot said he had no computer knowledge but was using a second-hand device that was controlled by cybercriminals.
Belot, who represents both Vinatier and Kasatkin, said Kasatkin had left France by plane and arrived back in Moscow on Thursday.
