The administrative court declared a case of that nature could only be challenged before the Council of State and Lyon has already indicated its intention to take the case there.
Lyon criticised the Ligue de Football Professionnel (LFP) for expressing satisfaction at the decision, saying in a statement on Saturday (AEST) that "the administrative tribunal did not rule on the merits of the case".
It added the development in "no way changes the nature and the basis of the action" brought by the club, which was sitting seventh when the season was halted.
The LFP said it "was pleased to learn that the appeals lodged by Olympique Lyonnais, Amiens SC and Toulouse FC were rejected by the summary judge of the Paris administrative court".
"In three orders issued on Friday afternoon [CET], the court ruled that the general decisions taken by the league's board of directors on 30 April could only be challenged before the Council of State," the LFP's statement added.
Lyon was denied European qualification via its league position because of the LFP's move to end the campaign with 10 matches still to play amid the coronavirus pandemic.
It can only secure a place in continental competition in 2020-2021 if it win the Coupe de France final, which is yet to be rescheduled, or the UEFA Champions League, which is also waiting for a restart plan.
Amiens and Toulouse were relegated by the LFP and have requested a 22-team Ligue 1 next season, rather than an increased Ligue 2.
The decision to end the campaign came after French prime minister Edouard Philippe declared there could be no major sporting events, including those behind closed doors, held before September.