The Conseil d'Etat - France's highest administrative court - ruled that there was "no serious doubt on the legality" of the decision taken by the Ligue de Football Professionnel (LFP) to call off the season on April 30.
Lyon and the determined Aulas had challenged that move, but now they must face up to the prospect of no European football next season, with their seventh position in the table frozen.
Many European leagues have resumed or are on the point of resuming; however, France's football authorities followed government advice in halting their campaign.
A Conseit d'Etat statement read: "The summary judge considers there is no serious doubt on the legality of this decision, which weighed the advantages and the disadvantages of an immediate stop of the championship, whereas a very great uncertainty affected the hypothesis of a possible restart of competitions in good time."
The court also backed the LFP's decision to confirm final placings based on points-per-game averages, and said the relegation of Amiens and Toulouse should be suspended.
That is not a full reprieve, and the relegation of both clubs could still be confirmed at a later date.
The court said the decision to demote Amiens and Toulouse could not be made on the premise that Ligue 1 is currently limited to 20 teams, given that agreement was due to end on June 30.
The LFP has been asked to review its format for the 2020-21 season, and in theory that could see this season's bottom two saved.
However, should the LFP, in conjunction with the French Football Federation (FFF), decide the league should remain at its current size, Amiens and Toulouse would likely face demotion to the second tier.
The Conseil d'Etat said: "The summary judge considers that the league's administrative board could not legally rely, in deciding to relegate the last two in the Ligue 1 ranking, on the fact that the current agreement reached with the French Football Federation (FFF) provides for a limit of 20 clubs, while this agreement ends on June 30 and a new agreement will have to be signed.
"The judge therefore orders the Ligue de Football Professionnel, in conjunction with the competent bodies of the FFF, to re-examine the question of the format of Ligue 1 for the 2020-2021 season, in light of all the elements relating to the conditions in which this season is likely to take place, and to draw the consequences as to the principle of relegation before June 30."