The ruling echoed an earlier one by the European Court of Justice (ECJ) which ordered the two governing bodies "to halt anti-competitive behaviour".
The court said FIFA and UEFA had imposed "unjustified and disproportionate restrictions" on free competition within the market, in a case filed by the promoters of the Super League.
Real Madrid and Barcelona are strong supporters of the project that most of Europe's other big clubs have abandoned.
The scope of the court's decision is uncertain, however, as it tackles regulations that have been completely rewritten in the interim period.
The case was brought before the Madrid Commercial Court by A22 Sports Management, the promoters of the three-tier, 80-club project.
A22 were buoyed after a decision by the Court of Justice of the European Union (ECJ) in December 2023, which also ruled that the ban on the Super League was contrary to European law, finding that UEFA did not have clear criteria for authorising or not authorising new competitions.
"It is not possible to impose a prohibition or restriction as a matter of principle, in other words to prohibit any other project in the future," explained judge Sofia Gil Garcia in her ruling on Monday, seen by AFP.
"To admit the contrary would be tantamount to accepting a kind of ban ... on any football competition project that competes with the current Champions League," continued the judge.
Spain were not among 26 European countries who signed a joint declaration against projects such as the Super League in February, stressing the need for "open" competition.
Proposed in 2021 by twelve elite European clubs, including Real Madrid and Barcelona, the first draft of the Super League project quickly collapsed, mainly due to fierce opposition from English clubs' fans and threats from UEFA and FIFA.
However, the project was relaunched this winter after the ECJ ruled that the powers of these two bodies were not "governed by any criteria ensuring that they are transparent, objective, non-discriminatory and proportionate".
UEFA has since corrected this 'shortcoming' with new, much more detailed regulations adopted in June 2022.
"This ruling does not mean that the so-called 'Super League' has been approved or validated," said UEFA in response to the ECJ ruling.
"The judgement is not final, nor does it bring anything new of significance," said La Liga chief Javier Tebas, firmly opposed to the Super League project.
