The 46-year-old was in attendance to witness his country win their first-ever Women's World Cup title in Sydney, where an Olga Carmona goal saw La Roja defeat England 1-0.
During the presentation ceremony, Rubiales embraced Pachuca striker Hermoso before kissing her on the lips - an act which Hermoso claimed she did not consent to, sparking global outrage.
Many male and female players stood in solidarity with Hermoso, and 81 Spain Women's players - including their entire World Cup-winning crop - announced their intention to boycott matches until Rubiales was removed from power.
Real Betis striker Borja Iglesias also stated that he would not represent his country while Rubiales remained in his post, but during a speech at the Extraordinary General Assembly, the 46-year-old - who has always said that the kiss was consensual - insisted on numerous occasions that he would not resign, drawing applause from men's head coach Luis de la Fuente and former women's manager Jorge Vilda.
During a bizarre address, Rubiales lashed out at "false feminists" and the "manhunt" against him, while his mother locked herself in a church on a hunger strike to protest against the "inhuman hunt" against her son.
Nevertheless, Rubiales was handed a provisional 90-day suspension by FIFA, and on Friday, the Spanish prosecutor filed a sexual assault and coercion complaint against the former president.
Now, the former defender has appeared on TalkTV with Piers Morgan to announce his resignation, although he continued to defend his actions and vowed to clear his name.
"I cannot continue my work. My father, my daughters, I spoke with them. They know it is not a question about me, some friends very close to me, and they say to me: Luis, now you have to focus on your dignity and to continue your life. Probably you are going to damage people you love," Rubiales said.
"After the rapid suspension by Fifa, and the rest of the proceedings against me, it's clear that I cannot return to my post. Trying to hang on in hope of clinging on won't result in anything positive for either the federation or Spanish football.
"I don't want Spanish football to be damaged because of a campaign as disproportionate as this one. I believe in the truth and I will do everything in my power to make sure it prevails.
"My daughters, my family and the people who love me have suffered the effects of excessive persecution, as well as many falsehoods, but it is also true that on the street, more and more every day, the truth is prevailing."
Rubiales - who was further denounced for grabbing his crotch in front of Queen Letizia and her 16-year-old daughter during the final - also served as vice-president of UEFA's executive committee, but he has stepped down from that role too.
Prior to Rubiales's resignation, the Spanish Football Federation had dismissed Vilda from his position as women's head coach - a decision which the 42-year-old labelled "unfair" and "unjust".
Montse Tome has taken over from Vilda as La Roja head coach, and the world champions are due to return to action against Sweden in the Nations League on September 22.