In its ruling seen by Reuters on Monday and dated September 1 - amid an unrelated scandal over Rubiales' behaviour at the Women's World Cup last month - the Madrid court said that "we are dealing with a pure exercise of the right to freely express an opinion about a person who, moreover, is a public figure".
The ruling can be appealed.
Rubiales declined to comment, and Clemente, who was Spain national men's team coach during the 1990s, was not available for comment.
Rubiales sued Clemente in 2022 after the outspoken coach said in an interview that Rubiales' "goal was to make a fortune" at the helm of the RFEF.
At the Aug. 20 medal ceremony following Spain's World Cup victory in Sydney, Rubiales grabbed player Jenni Hermoso's head and kissed her on the lips, triggering a furore over sexism in Spanish sport and society.
After weeks of defying calls from players, politicians and women's groups for him to step down, he finally resigned on Sept. 10 as president of the RFEF and from his position as vice president of UEFA, shortly after Hermoso filed a criminal complaint against him for alleged sexual assault.
Clemente, a former player, led Athletic Bilbao to La Liga titles before spending six years as manager of Spain, taking them to the 1994 and 1998 World Cups. He also coached the Serbia, Cameroon and Libya national teams.