The 34-year-old defender has signed a two-year deal after terminating his contract with Dalian Yifang earlier this week.
"I am very proud to join LOSC, a great French club," Fonte said.
"This is a new challenge for me, which I hope will be very successful. I will give everything to help the club as best as possible in its ambitious project."
The defender remained with Southampton as they worked their way back to the Premier League, and even managed to start four Europa League games for the club in 2015-16.
He moved to West Ham in January 2017 and played in 24 games in the Premier League with the London club over the next 13 months before joining Dalian Yifang in the China.
Despite making only nine appearances in China, he played every minute of Portugal's World Cup campaign this summer, which ended with a round of 16 loss to Uruguay for the reigning European Champions.
Lille finished 17th in Ligue 1 last term, avoiding a relegation play-off by one point.