Rubiales kissed the Spain forward during the presentation ceremony following the team's 1-0 win over England in Sunday's final.
"I didn't like it," Hermoso said on Instagram, but a statement released later on her behalf defended Rubiales.
On Monday, Rubiales said: "I was completely wrong, I have to admit it."
He added: "It was without bad intention at a time with a lot of excitement. In the moment, we saw it as natural, but outside a commotion has formed.
"I have to apologise, learn from this, and understand that when you are president you have to be more careful."
Rubiales had been criticised by some Spanish government ministers and come under fire on social media.
Spain's equalities minster Irene Montero said: "It's a form of sexual violence women suffer on a daily basis."
Montero added that up to now it had been "invisible" and that it is something "we can't normalise".
"We should not assume kissing without consent is something 'that happens'," she said.
Spain's sports minister Miquel Iceta told Spanish public radio it was "unacceptable" for Rubiales to kiss Hermoso, adding: "The first thing he has to do is to give explanations and make apologies, it is the logical and reasonable thing to do."
In a statement released by the Spanish football federation, following the player's initial comment about disliking the kiss, Hermoso said the moment was a "natural gesture of affection".
"It was a totally spontaneous mutual gesture because of the immense joy that winning a World Cup brings," said the 31-year-old, who is Spain's all-time leading scorer.
Video footage circulated online after the match also showed Rubiales, who was sat in the VIP area of the stadium near Fifa president Gianni Infantino and Queen Letzia of Spain, grab his groin in as he celebrated the final whistle.
Rubiales' actions were heavily criticised on social media, with 'dimision ya' - 'resign now' in English - trending on X, formerly known as Twitter, in Spain.
Rubiales told Spanish broadcaster COPE it was "a kiss between two friends celebrating something" and those who saw it differently were "idiots and stupid people".
"Let's ignore them and enjoy the good things," he added, before offering a different view on Monday.
Spanish newspaper El Pais ran the headline "Jenni didn't like Rubiales' kiss, neither did we".
Spain won the World Cup despite controversy over coach Jorge Vilda, who survived a player revolt to keep his job.
The RFEF said in September 2022 that 15 players had submitted identical emails saying they would not play for Vilda unless "significant" concerns over their "emotional state" and "health" were addressed.
However, the RFEF continued to back Vilda and posted 'VILDA IN' on Spain's official X account after their World Cup triumph.