The court in the southern Spanish city "decided to provisionally dismiss the case," indicating there "had been no signs of a crime," a spokesperson for the Andalusian High Court of Justice told AFP.
The plaintiff, named as 22-year-old reality TV personality Luisa Kremleva by various Spanish media outlets, can still appeal the decision.
Kremleva confirmed she has known Hernandez for "a long time" and posted pictures of injuries to her hands and knees on social media site Instagram claiming they had been caused by the footballer before later deleting the images.
Hernandez, currently owned by Atletico Madrid, was on holiday in the popular resort after an outstanding season on loan with Alaves, which has attracted the attention of European champions Real Madrid.
The left-back looks set to become the first player to cross the Madrid divide in 17 years with a €30 million ($34 million) fee reportedly having been agreed between the two clubs.
However, his decision to go on holiday following Alaves' 3-1 Copa del Rey final defeat to Barcelona had already drawn criticism as he had failed to report for duty with the French under-21 squad, "without explanation" according to coach Sylvain Ripoll.
Born in Marseille but raised in Spain, sports daily Marca reported this week that the player wants to play his international football for Spain.
His elder brother Lucas Hernandez, 21, also an Atletico player, was ordered to do 31 days of community service alongside his ex-girlfriend following a case of domestic violence in February.
He was also ordered not to contact the woman for a period of six months.