Heading into the last round, Lille and Brest were level on points behind already-crowned champion Paris Saint-Germain and Monaco, with Lille ahead only by a difference of two goals.
Lille looked set for a third place finish but blew a 2-1 lead against Nice in added time to draw 2-2, dropping into fourth place.
After the expansion of Europe's top club competition from next season, the French league will have three automatic spots in the tournament rather than two. Brest, whose attack-minded approach developed by coach Eric Roy has been a pleasure for fans to watch this season, will play in Europe for the first time.
The club stadium holds 15,000 compared to PSG's capacity of nearly 49,000 at Parc des Princes, while PSG's yearly budget of 700 million euros dwarfs Brest's 48 million euros — among the smallest in the league.
Lille captain Benjamin Andre thought he had scored the winner in the 73rd minute with a powerful header from a corner but the hosts could not hold onto their lead as Jordan Lotomba put a header between the legs of Lille goalkeeper Vito Mannone.
Roy has done a remarkable rebuilding job at Brest. The team were in the relegation zone when he was hired midway through last season and finished 14th. Roy had been 12 years without a coaching job.
Mahdi Camara, Jordan Amavi and Kenny Lala scored Brest's goals.
Already crowned champion for a record-extending 12th time, PSG concluded their campaign with a 2-0 win at Metz that condemned the hosts to a relegation playoff.
Carlos Soler and Lee Kang-in scored PSG's goals.
PSG finished top of the league with 76 points, nine more than second-place Monaco, who thrashed Nantes 4-0.
PSG were without star striker Kylian Mbappé, who was left out of the squad for the final league game amid media reports that he spent the weekend at the Cannes film festival.
Mbappé is leaving PSG after seven seasons at the French league club. Ousmane Dembélé, Vitinha, Marquinhos, Fabian Ruiz and Gianluigi Donnarumma also sat out the trip to Metz. Unless PSG coach Luis Enrique decides to snub him, Mbappé will have a final occasion to play with PSG in the French Cup final on May 25 against Lyon.
Lyon captain Alexandre Lacazette scored a brace in a 2-1 win over Strasbourg to help Lyon finish in sixth place ahead of Lens, who were held 2-2 at home by Montpellier. Lyon qualified for the Europa League.
Nine-time champions Marseille concluded a mediocre season with a rare victory on the road, a 2-1 win at Le Havre.
In a contest between two teams that will be demoted to the second-tier of French soccer next season, Lorient demolished last-place Clermont 5-0.
