The Bluebirds say they paid off the final two scheduled payments, believed to total around £12m.
But Cardiff have made it clear they will continue legal action against FC Nantes through the French courts.
The Championship club paid the first instalment of Sala’s transfer fee in January.
“Cardiff City today paid the second and third instalments of the transfer fee for Emiliano Sala, as recently ordered to do by Fifa,” a Cardiff statement said.
“This is despite there not yet being a judicial decision about FC Nantes’ liability for the crash. We continue to work towards those responsible being held accountable.
“We look forward to the trial before the French court next year.”
Cardiff City: Football club told to pay Sala transfer balance
Cardiff have been in dispute with FC Nantes over the transfer fee since the striker died on route to Wales in January 2019.
The Argentine had become Cardiff’s record £15m record signing when the plane carrying him from France to the Welsh capital crashed into the English Channel.
A three-window embargo was imposed by world football’s governing body Fifa because of Cardiff’s refusal to pay the first instalment of the transfer fee they had agreed with FCNantes.
Cardiff claimed they were not liable for any of the fee because Sala was not officially their player when he died at the age of 28.
Cardiff then failed in an appeal over the Fifa ruling to the Court of Arbitration for Sport (CAS) in Lausanne in 2022.
In January, the club paid FC Nantes the first instalment of the fee. Fifa then lifted the embargo on the club.
The English Football League also put an embargo on Cardiff and remnants of that remain in place, as the club are currently unable to pay fees for new signings.
The block on paying for players had been due to stretch until next summer, but the length of the embargo has been reduced and it will be lifted in January 2024, when Cardiff will again be allowed to pay for players.
But Cardiff’s action in the French civil courts will still be pursued after a Swiss Federal Tribunal decided the CAS did not have the power to deal with the club’s claim for damages.
In May, Cardiff began suing FC Nantes for almost £100m over the death of Sala.