The 46-year-old came under fire for kissing Spain player Jenni Hermoso on the lips at the Women's World Cup final last month.
Hermoso said that the kiss during the presentation ceremony after Spain's win over England was not consensual and has since filed a legal complaint against Rubiales.
Rubiales has now left his position, revealing the news in a world exclusive with Piers Morgan on TalkTV.
"I love so much my daughters and they love me so, so much. I am very happy and very proud of them. They are very near to me," Rubiales said on Piers Morgan: Uncensored.
"About my resignation, yes, I am going to do [it]…"
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Morgan responded: "You're going to resign?"
Rubiales replied: "Yes, because I cannot continue in my work."
"Yeah, my father, my daughters, I spoke with them and they know it's not a question about me," Rubiales continued.
"Some friends, very close to me, and they say to me, 'Luis, now you have to focus on dignity and to continue your life because if not, probably, you are going to damage people you love, the sport you love…'"
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"When someone is not thinking only about himself, because I had to support a lot in this three weeks, but this is more a question of not only me and being an attitude of me can affect third parties very importantly. In this situation now it is more intelligent and the thing I had to do," Rubiales added.
Rubiales had already been provisionally banned from all football activity for an initial 90 days by FIFA while it investigates his conduct at the final.
He's facing criminal charges in addition to the ongoing inquiry by Spain's top sport court for 'serious misconduct' following Hermoso filing her complaint to the prosecutor's office on Wednesday.
Rubiales could face a fine or prison sentence of one to four years if found guilty of sexual assault.
Prosecutors said on Friday that Rubiales could've committed an act of coercion when, according to Hermoso, he pressured her to speak out in his defence in the immediate aftermath of the incident.
The judge has also been asked by prosecutors for Rubiales to appear before a court at a preliminary testimony.
If the National Court judge agrees, it would lead to a formal court investigation that will end with a recommendation for the case to either be dismissed or go to trial.
Hermoso says she did not want to be kissed and that she felt 'vulnerable and a victim of aggression'. The player also claims that she and her family were pressured by the federation to show support for Rubiales immediately after the incident.
However, regional FA leaders called for Rubiales' removal. Meanwhile, Pedro Rocha, the federation's interim president, apologised this week for the 'enormous damage' caused by his predecessor's actions and vowed a organisational restructure.
Jorge Vilda, who was seen applauding Rubiales during the speech in which he refused to resign, was sacked on Tuesday and replaced by his former assistant Montse Tome.
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For the full interview, with more stunning revelations tune in to Piers Morgan Uncensored on Tuesday at 8pm.
Watch Piers Morgan Uncensored, Monday to Thursday on TalkTV at 8pm. Available on Sky 522, Sky Glass 508, Virgin Media 606, Freeview 237 and Freesat 217 as well as on DAB, Amazon Fire TV, Apple TV, Samsung TV Plus, YouTube, the Talk.TV website and TalkTV iOS and Android apps.
More will follow. For the latest on this and other breaking news stories, listen to talkSPORT