FIFA, the soccer world’s governing body, said on Saturday that it had provisionally suspended Luis Rubiales, president of Spain’s soccer federation, amid an investigation that he forcibly kissed the player Jennifer Hermoso after Spain’s Women’s World Cup victory last Sunday.

In a statement, FIFA said that Mr. Rubiales would be suspended “from all football-related activities” at national and international levels for an initial period of 90 days, starting Saturday. The body also ordered both Mr. Rubiales and the soccer federation he chairs to refrain from contacting Ms. Hermoso, a star forward on Spain’s winning national team.

The decision came less than a day after Spain’s soccer federation said it would stand by Mr. Rubiales, who has insisted he did nothing wrong to Ms. Hermoso, and threatened legal action to protect the reputation of its president.

Mr. Rubiales’s kiss at the Women’s World Cup medals ceremony last weekend in Australia — broadcast live to millions — cast a pall over the Spanish team’s celebrations, drawing attention away from a proud national moment and toward a legacy of sexism scandals in Spanish soccer. Ms. Hermoso said she had never consented to the kiss but had faced pressure to publicly back Mr. Rubiales initially and downplay his actions.

“I felt vulnerable and the victim of an impulse-driven, sexist, out-of-place act without any consent on my part,” she said in a statement on Friday. Futpro, Spain’s main union of professional female soccer players, has supported Ms. Hermoso and criticized Mr. Rubiales’s behavior, as have several Spanish soccer clubs.

Many thought Mr. Rubiales, who called the kiss a consensual “peck” during a speech, would resign, putting an end to the controversy. His refusal to do so fueled outrage in a country that views the fight against sexism as a societal priority. Leading politicians, including government ministers, have condemned his behavior and called for him to step down.

On Saturday, before FIFA announced its decision, Spain’s top sporting body filed a formal complaint against Mr. Rubiales — who is also a vice president of the UEFA, European soccer’s governing body — in an administrative court that handles sporting disputes, accusing him of abusing his authority and violating public sports decorum.

“We are ready for this to be the #MeToo of Spanish football and for this to be a change,” Victor Francos Díaz, who directs Spain’s National Sports Council, told reporters Friday ahead of filing the complaint.

Both the kiss and the federation’s forceful defense of its embattled president have prompted debate over a history of accusations of misogyny in Spanish soccer. The previous head coach of the women’s national soccer team, Ignacio Quereda, served for 27 years before being ousted amid allegations of sexism.

“This situation has caused structural damage not only to women’s soccer, but also to sport in general and to the values it transmits to society,” said Dolors Ribalta Alcalde, a specialist in women’s soccer at Ramon Llull University in Barcelona.

But in a statement released late Friday, Spain’s soccer federation pushed back, vowing to take “as many legal actions as are appropriate in defense of the president’s honor” in response to Ms. Hermoso’s account of what happened after Spain’s 1-0 victory over England last Sunday.

And in a speech delivered at a meeting of the Spanish soccer federation earlier Friday, Mr. Rubiales defended himself by saying that the kiss had been “spontaneous, mutual, euphoric and consensual.” He accused his detractors of practicing “false feminism” in an attempt to tear him down, drawing applause from the mostly male audience.

Mr. Rubiales said that Ms. Hermoso, as she lined up onstage to collect her medal, “was the one who lifted me in her arms and brought me close to her body.” Then, according to Mr. Rubiales’s account, he asked if he could give her a small kiss and she said “Vale,” or “OK.”

Ms. Hermoso is widely regarded as one of the best forwards in women’s soccer today, and she holds the record for the number of goals scored with the Spanish national team. She initially downplayed the kiss, saying it had been a “spontaneous mutual gesture.”

But she added in her statement on Friday that she had been under pressure from the Spanish soccer federation “to give a testimony that had little or nothing to do with my feelings.” In a post-match video, she could be heard voicing her distaste: “Hey, but I didn’t like that!”

Mr. Rubiales has also been criticized after video appeared to show him grabbing his genitals with both hands to celebrate Spain’s victory. (He later apologized.)

A career soccer player raised in Grenada, Mr. Rubiales never became a household name. But he eventually rose through the ranks off the field — first becoming the chief of the Spanish players’ association in 2010 and eventually federation head in 2018.

Many in Spain — including in its vaunted soccer community — denounced Mr. Rubiales’s actions and issued public statements of solidarity. Players on the Spanish women’s team, along with dozens of others, have said they will refuse to play for the national squad until “the current leaders,” including Mr. Rubiales, are gone.

Xavi Hernández, the coach of FC Barcelona, said during a pregame news conference on Saturday that Mr. Rubiales’s behavior was “totally unacceptable” and “inadmissible.”

Politicians across the political spectrum also fiercely criticized Mr. Rubiales.

“Mr. Rubiales still does not understand where he is or what he has done,” Yolanda Díaz, Spain’s labor minister, said on social media. “You should resign now and save us the embarrassment.”

A soccer match dedicated to Mr. Rubiales was canceled in Motril, his hometown, by local authorities to head off potential disturbances.

In its statement released Friday, Spain’s soccer federation provided four images of the embrace, asserting that they were visual proof of Mr. Rubiales’s version of events.

Dr. Ribalta, the sports academic, described Mr. Rubiales’s behavior — both the kiss and his response to the outcry — as the culmination of years of mistreatment of female players.

Spain’s women’s national team long lacked elite training facilities and even jerseys designed to be worn by women. Most recently, 15 players revolted last year against their coach, Jorge Vilda, and the federation, complaining of outdated training methods and controlling behavior.

“We’ve reached a key moment when changes need to be implemented,” Dr. Ribalta said.