Bafetimbi Gomis and Miralem Pjanic netted as Lyon finished on 72 points, six behind champions Olympique Marseille who beat bottom club Grenoble 2-0.
"It's amazing, nowhere is there as much passion as in Marseille. It's fabulous, fantastic for the players, I'm so proud to be their coach," Didier Deschamps told Canal Plus TV as his players were presented with the trophy.
Senegal striker Mamadou Niang converted a Marseille penalty five minutes before the interval to finish as Ligue 1's top scorer with 18 goals. Hatem Ben Arfa made it 2-0 from 25 metres in stoppage time.
Lyon's fans also had something to cheer when their team made light work of Le Mans to secure their 11th straight participation in the Champions League.
"Some good results this season gave us confidence and we knew anything was possible tonight," said captain Benoit Pedretti.
"I feel very sorry for the fans, for the club, for my team mates," said midfielder Yohan Cabaye.
Cabaye missed a second-half penalty after Lorient striker Kevin Gameiro had cancelled out Ricardo Costa's opener. Yann Jouffre struck the winner for the home team in the 65th minute.
Last year's Ligue 1 champions Girondins Bordeaux, who lost 4-3 at Racing Lens, ended up sixth and will not play in Europe next season.
Coach Laurent Blanc, widely tipped as Raymond Domenech's successor for the France job, declined to say whether he would stay at the club next season.
"You will know nothing about my future tonight," he told a news conference.
