Pedro Almodovar's movie gained a massive 16 nominations ahead of the glitzy prizegiving, but lost out in several categories to cop drama No Rest for the Wicked, which won Best Film, Best Director for Enrique Urbizu, and Best original screenplay, while Jose Coronado trumped Banderas to take the Best Actor trophy.
The Skin I Live In, which won the Best Foreign Language Film prize at the recent British Academy of Film and Television Arts (BAFTA) Awards, triumphed in four categories.
Elena Anaya took the Best Actress trophy and Jan Cornet was named Best Breakthrough Actor, while the film also scooped awards for make-up and original music.
Oscar-tipped silent movie The Artist was also honoured at the ceremony in Madrid, winning the award for Best European Film.
It's 1828 and an 82-year-old Goya (Francisco Rabal) lives out his remaining days in Bordeaux France. Nursed by his strong-willed young daughter (Dafne Fernández) he relates tales of his many adventures in art politics and love - especially those concerning his stormy romance with the danger-loving Duchess of Alba (Maribel Verdú). And that's as much of a plot as this image-driven film cares to offer while meandering along with the logic of a melancholy dream.
Spanish screen veteran Rabal ("Tie Me Up! Tie Me Down!") lends his titanic presence to a role that basically boils down to parading around in a nightshirt with a haunted look on his face. Jose Coronado ("La Mirada del Otro") has slightly more to work with as a younger Goya caught up in vague bits of court intrigue while he follows in Velázquez's footsteps as Spain's most famous artist of the period. He and the offbeatly foxy Verdú ("Belle Epoque") briefly threaten to jump-start the narrative with a torrid affair then Verd£'s Duchess character is unsatisfyingly written out of the picture.
Writer-director Carlos Saura's 30th film displays his usual flair for striking imagery but the innovative style he develops in his fourth outing with acclaimed cinematographer Vittorio Storaro could have used a bit more dramatic meat to hang on. In the film's intentionally nonrealistic world actors march in front of painted backdrops to form moving tableaux vivants. Semi-transparent fabric screens reveal people walking on the other side of walls and elements of Goya's artworks suddenly come to life - all of which is more interesting than what is happening to the characters.