Rubiales had until last night refused to resign despite an outcry in the wake of the incident in the aftermath of the Spain's 1-0 triumph against England in the final in Sydney on 20 August.
Last week Jenni Hermoso, the midfielder who was kissed by Rubiales, filed a complaint against him for sexual assault.
On Friday it was followed by a prosecutor filing a complaint with Spain's high court against the man who has been at the top of Spanish football's domestic organisation for five years.
It said that there could be grounds to charge him with sexual assault as well as coercion.
Rubiales told Piers Morgan in an interview on Talk TV that he would step down. He said: "About my resignation- yes I am going to do it. I cannot continue my work. My father, my daughters, I spoke with them.
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