Rubiales announced his resignation in a statement in which he said his position had become untenable, with the Spanish Football Federation (RFEF) later confirming he had sent a resignation letter to acting president Pedro Rocha.
His kiss of player Jenni Hermoso after the World Cup win in Sydney on Aug. 20 had caused outrage among players, government officials and many in wider Spanish society and raised questions over sexism in sport.
His decision to go came after further blows to his position in the last few days.
A Spanish prosecutor filed a complaint with the High Court against Rubiales on Friday for sexual assault and coercion.
I guess he scored an own goal.