During the post-match ceremony at the Stadium Australia, Hermoso was receiving her gold media when Rubiales suddenly put both hands on her head before giving her a surprise kiss on the lips, according to CNN.
The incident was captured on camera and quickly went viral on social media, prompting criticism of Rubiales.
In an Instagram live afterwards, Hermoso was asked about the incident and she said she "didn’t like it."
"But what am I supposed to do?" Hermoso responded to another question.
Later on, Hermoso clarified the incident.
"It was a totally spontaneous mutual gesture because of the immense joy that winning a World Cup brings. The president and I have a great relationship, his behaviour with all of us has been outstanding and it was a natural gesture of affection and gratitude." Hermoso told AFP.
Rubiales later told Radio Marca that it was just an "unimportant gesture of affection".
Hermoso was not the only Spanish player that Rubiales kissed during the post-match ceremony, as a video showed Rubiales kissing other members of the squad on the cheeks and embracing them after they received their medals.
Alberto Ortega of Spanish newspaper El Confidencial posted on Twitter: "Rubiales taking the trophy from the players to give it to Queen Leticia and kissing Jennifer Hermoso on the mouth is simply disgusting."
On Sunday night, Spain defeated England 1-0, with the goal scored by Olga Carmona to clinch their first-ever Women’s World Cup title.