Hermoso gave her testimony on Tuesday and the complaint will be processed "as soon as possible", the prosecutor added.
With the complaint, Rubiales could face criminal charges in addition to the ongoing inquiry by Spain's top sports court for "serious misconduct" and an investigation by world soccer governing body FIFA, which has provisionally suspended Rubiales from office.
Neither Hermoso's representatives nor Rubiales were immediately available for comment.
Rubiales grabbed Hermoso's head and kissed her on the lips during the medal-giving ceremony that followed Spain's 1-0 victory over England in the Women's World Cup final on August 20th.
Late last month, the prosecutor for Spain's High Court said Rubiales could face a sexual assault charge, which carries a prison term of between one and four years if Hermoso were to file a complaint.
The High Court has jurisdiction over the case as the incident took place abroad - in Sydney, Australia.
Hermoso said she did not want to be kissed, and that she felt "vulnerable and a victim of an aggression".
Rubiales, who has so far refused to resign despite heavy pressure, said the kiss was "spontaneous, mutual, euphoric and consensual".
Rubiales' behaviour has sparked outrage in Spain and abroad. He also grabbed his crotch while standing close to Spain's Queen Letizia and her 16-year-old daughter during the final match.
The Spanish men's team criticised the country's soccer boss on Monday for his "unacceptable behaviour", but one of the team's captains, Real Madrid defender Dani Carvajal, sparked criticism later for arguably questioning Hermoso's status as a victim in an interview for Spanish radio Onda Cero.
"There are legal bodies that are considering whether Jennifer is really a victim of something that is being investigated. There are people who have to decide whether there is an offender and a victim," Carvajal said on Tuesday.
"So we can't take a position or condemn one side or the other beforehand without really knowing what has happened, what has been stipulated because Jennifer has not yet filed a complaint," he added, unaware that Hermoso had met with prosecutors and filed a criminal complaint earlier in the day.
In an effort to explain his words in a press conference on Wednesday, Carvajal went further and said that "Rubiales should be supported in the same way as Jenni Hermoso" in this process.
"I can understand that Jenni is going through a bad time, we have to show my solidarity. However, I don't think the president is having a good time either. I am not here to judge anyone," Carvajal said.
"The presumption of innocence is a constitutional right. You cannot victimise or blame anyone."
Women's team coach Jorge Vilda, a close ally of Rubiales, was sacked on Tuesday. The RFEF later announced it had appointed Montse Tome to succeed Vilda, making her the first woman to manage the side.
