Almodovar was absent from the ceremony, but his film won five prizes including best film, director, original music, actress for Penelope Cruz and supporting actress for Carmen Maura.
Labyrinth (El Laberinto Del Fauno) won seven Goyas, including original script for del Toro, best new actress for the young Ivana Baquero, cinematography, special effects, editing, sound and hair and make-up.
Of Labyrinth's whopping six Oscar nominations this year, three are in these same categories - screenplay, cinematography and make-up. The Spanish-Mexican co-production also earned a best foreign language film nomination for the Oscars representing Mexico, while Almodovar, Spain's nominee, did not make the final cut.
Del Toro thanked the Almodovar brothers for their hand in his success with Labryinth as producers on his previous Spain-shot film, 2001's The Devil's Backbone (El Espinazo Del Diablo). He also gave a nod to co-productions in general: 'Mexico and Spain: together we do it better.'
Agustin Diaz-Yanes' big-budget box office hit Alatriste, which went into the night with the most nominations including in all the top categories, went home with three statues: art direction, production design and wardrobe. Also multiply nominated in top categories, Mediapro-backed biopic Salvador won best adapted script, its sole Goya from 11 nominations.
Alatriste star Viggo Mortensen and Salvador lead Daniel Bruehl, both in the Madrid audience, were beaten out for best actor kudos by veteran Juan Diego (Vete De Mi), the least internationally known of the nominees, which also included Labryinth's Sergi Lopez. Diego previously picked up a best actor prize for the same role at September's Donostia-San Sebastian International Film Festival.
Near tears as she accepted her best actress prize and later returned to read Almodovar's acceptance speech for best director, Cruz picked up her Goya just days after her history-making nomination for a best actress Oscar.
Sleeper hit DarkBlueAlmostBlack (AzulOscuroCasiNegro) won three key awards, including best new director for Daniel Sanchez Arevalo, best supporting actor for Antonio de la Torre and best new actor for Quim Gutierrez.
This year's nominations reflected a singular parity with Spanish audiences' tastes - Alatriste, Volver and Pan's Labyrinth were the three top-grossing films in Spain last year.
Filmax-Patagonik co-production The Hairy Tooth Fairy took home a best animated feature nod, while Carlos Benito's Filmmakers In Action (Cineastas En Accion) won best documentary.
Stephen Frears' The Queen picked up the Goya for best European film, while Argentina's Las Manos won best foreign Spanish-language film.