The Spaniard dominated proceedings from the off despite the strength of the field, which included the likes of Edwina Tops-Alexander and Jeroen Dubbeldam.
Just three riders completed the first round without penalties: Moya, his compatriot Pilar Lucrecia Cordon Muro and the Belgian Philippe Le Jeune.
Cordon Muro and Le Jeune failed to maintain their momentum, however, both riders sending a rail down in the second round, while the imperious Alvarez Moya did not flinch, going on to register the only double clear of the class.
Frenchman Michel Robert with Oh d'Eole claimed second but will likely regret having neglected the clock in their first round, which cost them a penalty point.
Swiss rider Steve Guerdat with Sydney VIIII completed the podium after going quickest in the second round.
American Richard Spooner, who was looking to repeat his 2011 victory in La Coruna, knocked a rail down in the first round that eventually saw him finish in fourth place.