Thauvin signed for Lille from Bastia in January, but departs without having made an appearance.
The winger, 20, initially joined Bastia on loan immediately after leaving and refused to play for Lille this term as he sought another transfer.
He played 32 times for Bastia in the league last term, scoring 10 goals, catching the eye with some stunning late-season form - in which he scored six times in his last eight appearances of the campaign.
"We are obviously very pleased to have found a positive outcome to this long negotiation with our counterparts in Lille," said Marseille president Vincent Labrune.
"I take this opportunity to underline the courtesy and the quality of the exchanges I have had these days with (Lille president) Michel Seydoux. They have allowed us to achieve this successful outcome.
"Finally, and most importantly, we are delighted that Florian can bring all his talent to our team.
"He has all the qualities to win the heart of our supporters."
