Real Madrid snatched a 1-1 draw with Valencia at the Bernabeu in February when referee Pedro Tristante Oliva awarded a controversial injury-time penalty for a Carlos Marchena push on Real striker Raul.
The decision created a storm in Spain with Valencia officials describing the decision as a joke and commentators across the country openly accusing Spain's Football Federation of bias in favour of Real Madrid.
Despite the result Valencia went on to take the league title but around 100 club members and shareholders nevertheless presented a case against the referee claiming he had been negligent.
A Valencia court decided this week that the case would be heard.
According to the group's lawyer Andres Sanchis the referee and the Football Federation have been given 20 days to make statements and the judge will rule in three or four months' time.
The fans are seeking damages equivalent to their costs in bringing the case Sanchis said.