Proposed in 2021 by 12 elite European clubs, including Real Madrid and Barcelona, the Super League project quickly collapsed due to fierce opposition from English clubs' fans and threats from UEFA and FIFA.
The European Court of Justice (ECJ) ruled in December 2023 that the ban on the Super League was contrary to European law.
Last year, a Spanish judge said FIFA and UEFA had "prevented free competition" by opposing the Super League, ruling they were practising anti-competitive behaviour and abusing their dominant position.
The court in Madrid on Wednesday also rejected appeals filed by La Liga and the Spanish football federation.
The scope of the court's decision is uncertain, however, as it tackles regulations that have been completely rewritten in the interim period.
Real Madrid said they were "delighted" by the ruling, "confirming that UEFA, in the matter of the Super League, seriously infringed the European Union's free competition rules... by abusing its dominant position".
"The club announces that it will continue to work for the good of global football and fans, while claiming substantial damages from UEFA," Real Madrid said in a statement.