France's highest administrative court on Tuesday blocked the relegation of Amiens and Toulouse from Ligue 1 while rejecting Lyon's appeal against the decision to declare the season over.
The judge in the Council of State "validates the end of the season and the standings but suspends relegation", read a statement summarising the ruling.
The French league (LFP) brought a premature end to the campaign in late April due to the coronavirus pandemic.
"I feel like football's values have won. For every employee, those in the academy, professional players, it's extraordinary because they are people and families who were scared they would lose their jobs," Amiens president Bernard Joannin told AFP.
"It's a big satisfaction, I always said the league's decision was unfair and incoherent."
The decision to call the season off with 10 rounds of matches unplayed followed an announcement by the French government that football could not restart because of the health crisis.
The judge also ordered the LFP to re-examine with the French football federation the proposed format for the top division next season, which could feature 22 teams in Ligue 1 -- two more than usual.
Amiens and Toulouse argued their relegation from the top-flight was "unjust and "arbitrary" while Lyon president Jean-Michel Aulas was the leading voice against the decision to end the season early.
Lyon, who have reached this season's Champions League last 16, were left seventh in the table and outside the European qualification places when the season was halted.
Paris Saint-Germain were declared champions for the seventh time in eight years.
"The decision to proceed to final standings in Ligue 1 and Ligue 2 doesn't necessarily lead, by itself, to the relegation to Ligue 2 of the bottom two in Ligue 1, nor the promotion to Ligue 1 of the top two in Ligue 2," the court ruling said.
The league ranked teams by the ratio of points won to games played, but that did not change any of the placings in the final table.
Toulouse, bottom for many months and with only three wins and 13 points from 28 games, were 14 points from potential safety.
Amiens were 10 points better off, but still four points away from the lifeline of a play-off spot.
Lorient and Lens were promoted in their place, while the usual promotion and relegation play-offs were ditched.