FIFA says Cardiff must pay 6 million euros (NZ $10.38 million) to Nantes as a first installment of the transfer fee for Emiliano Sala, agreed in January before he died in an airplane crash.
FIFA says its players' status panel "never lost sight of the specific and unique circumstances of this tragic situation" in the dispute between the two clubs.
The FIFA ruling suggests Cardiff will also be liable for subsequent payments in the Argentine forward's 15 million pounds (about $32 million) transfer deal.
FIFA says Cardiff can appeal its verdict to the Court of Arbitration for Sport.
Nantes filed a complaint with FIFA when Cardiff disputed paying for Sala, who was killed before playing for his new club.
The single-engine aircraft with Sala and pilot David Ibbotson crashed in the English Channel while flying from Nantes to Cardiff.