Monaco finished runners-up to Paris St Germain after their 3-0 win at Troyes sent their opponents down to Ligue 2, while Lyon ended third after coming from behind to beat Nice 3-2, thanks to Memphis Depay's treble.
Fourth-placed Marseille, who lost to Atletico Madrid in the Europa League final on Wednesday, beat visiting Amiens 2-1 but it was not enough to put them on the podium.
They end up with 77 points, one behind Lyon, while Monaco have 80.
News that makes sense
Your trusted source for staying up-to-date with the world around you. Get free daily news updates and analysis, straight to your inbox.
But PSG, who had already been crowned, finished well clear on 93 points after a 0-0 draw at Caen that kept the Normandy side in the elite.
Marseille will play in the Europa League, along with fifth-placed Stade Rennais and sixth-placed Girondins de Bordeaux, who respectively drew 1-1 at home to Montpellier and won 4-0 at Metz.
Troyes join bottom club Metz in Ligue 2 while Toulouse beat En Avant Guingamp 2-1 to finish 18th and will play either AC Ajaccio or Le Havre in a playoff.
The game between Ajaccio and Le Havre, due to be played on Friday, was postponed until Sunday after fans attacked the Le Havre bus, the French League said on Saturday, condemning "serious incidents".
Monaco needed a draw to secure a Champions League spot but went further, defeating Troyes.
Rony Lopes beat Erwin Zelazny on 21 minutes after the keeper had parried Youri Telemans' shot into the Portugal striker's path.
Lopes made sure there would be no late drama when he scored again with a low shot in the 71st minute and Jordi Mboul added a third in stoppage time.
At Lyon's Groupama stadium, Nice went ahead in the 18th minute when Alassane Plea collected a fine through ball from Mario Balotelli and shot between keeper Mathieu Gorgelin's legs.
Lyon hit the woodwork before the break, but Depay struck three times in the second half.
The Dutch striker poked the ball home from Nabil Fekir's cross in the 48th minute and he made it 2-1 on 65 minutes with a low free kick that went under the wall.
Four minutes before time, Depay chipped the ball past Walter Benitez to wrap up the game. Plea pulled one back two minutes later with a powerful strike for his second of the game.
Marseille, too, did what they needed to, but it proved to be in vain.
They opened the scoring after 10 minutes when Morgan Sanson found the back of the net with a half-volley from inside the box.
They doubled the tally eight minutes later, Kostas Mitroglou heading home from Lucas Ocampos's cross. Amiens reduced the arrears on the half-hour when Moussa Konate beat Steve Mandanda from close range.
But while Marseille hung on, it was not enough to take them into a Champions League place.
(Reporting by Julien Pretot; Editing by Neville Dalton)
