The club says the ruling means Barcelona and the presidents are no longer defendants in the case involving the Brazilian striker.
The club said in a statement on Thursday that new charges would have to be brought up in Barcelona for the case against them to continue.
A Brazilian investment group has claimed it was financially damaged because Barcelona and Neymar allegedly withheld the real amount of the player's transfer fee from Brazilian club Santos.
Neymar and his father appeared before a court last month and maintained their innocence.
The case has been transferred from a Madrid court to Barcelona.
Related story
Barcelona football player Messi loses appeal in tax fraud trial
