England manager Sarina Wiegman dedicated her Uefa Women's Coach of the Year award to World Cup winners Spain, as Fifa president Gianni Infantino said their success had been "spoiled".
Spanish football federation president Luis Rubiales has been widely criticised for kissing forward Jenni Hermoso on the lips after the final.
Wiegman said the victorious Spain players "deserve to be listened to".
And Infantino wrote on social media: "This should never have happened."
Hermoso said the kiss during the presentation ceremony after the World Cup final win over England in Sydney on 20 August was not consensual.
Rubiales was suspended by world football's governing body Fifa on Saturday but has repeatedly refused to resign.
Wiegman led the audience at Thursday's ceremony in a round of applause for Spain, stating they "deserve to be celebrated".
"We all know the issues around the Spanish team," she said.
"It really hurts me as a coach, a mother of two daughters, as a wife and human being. And it shows, the game has grown so much, but there is a long way to go in women's football and society.
"I would like to dedicate this award to the Spanish team, the team that played such great football that everyone enjoyed."
Infantino later posted a photograph of himself with the world champions on Instagram, writing: "Sadly, the well-deserved celebrations for these magnificent champions were spoiled by what happened after the final whistle.
"Fifa's disciplinary bodies immediately assumed responsibility and took the necessary actions.
"On our side, we should continue to focus on how further to support women and women's football in future, both on and off the pitch."
Infantino was criticised for a speech he gave at the World Cup where he said women who "pick the right fights" can "convince us men what we have to do" to bring progress in women's football.
We must not allow such abuses of power - Bonmati
The incident has sparked a global conversation about consent and power, with widespread protests taking place across Spain in support of Hermoso.
The forward's international team-mate Aitana Bonmati also spoke about the incident as she accepted her women's player of the year award at the Uefa event.
"Thanks to Sarina for her words. These are not very good times just now for Spanish football," the 25-year-old midfielder said.
"We have just won the World Cup but that is not really being spoken about because things have happened that I wish were not happening.
"As a society, we must not allow such abuses of power in a working relationship or such a lack of respect."
Spanish football federation regional leaders have called on president Rubiales to immediately step down, while Spanish prosecutors opened a preliminary investigation into whether the incident amounts to a crime of sexual assault.
Spain's Sports Tribunal (TAD) also met on Monday to discuss the Spanish government's request to suspend Rubiales, with a decision yet to be announced.
Football 'has a women's problem'
Meanwhile, Chelsea women's manager Emma Hayes says she is hopeful the situation will prove to be a "huge wake-up moment" in Spain.
"This is not just an isolated incident," said Hayes, speaking on Woman's Hour on BBC Radio 4.
"It is about a systemic problem over a number of years where the women's national team have complained on more than one occasion about the level of treatment and equality of opportunity and access for all of them.
"I hope that it will bring seismic and systemic change and you can see with the reaction across Spain it is certainly in support of Jenni Hermoso and the entire Spanish team.
"This is a huge wake-up moment for Spanish society and it goes beyond Spanish football about how women feel they are treated or mistreated.
"It [misogyny] happens here as much as Spain. I have to deal with it on a regular basis. Do I think we are much further ahead than Spain? Yes. But we still have so much work to do.
"Of course it [football] has a 'women's problem'. We have to look at some of the work done to challenge the same issues around racism because some people are not aware of how inherently misogynist they are.
"We are making strides in the right direction but we want to keep progressing."