The 42-year-old guided his nation to their first-ever World Cup crown at the recently-concluded 2023 tournament, as La Roja defeated England 1-0 in the final.
However, Spain's triumph was tarnished by two off-field scandals, as Vilda faced a player revolt in late 2022 amid alleged concerns over his training styles and treatment of players.
The former Under-17s and Under-19s head coach refused to step down from his role in the wake of the accusations, and 12 of the 15 players who originally boycotted national team duty did not return for the World Cup.
During La Roja's celebrations, RFEF president Luis Rubiales sparked global outcry by kissing striker Jenni Hermoso on the lips - an act that the Pachuca player claimed was not consensual.
In contrast, a bullish Rubiales has consistently stated that Hermoso did consent to the kiss and has so far resisted calls to step down from his role, which Vilda expressed his support for during an explosive General Assembly speech.
As Rubiales - who has been provisionally suspended for 90 days by FIFA - said on numerous occasions that he would not leave his post, Vilda was seen applauding his superior, although the 42-year-old subsequently labelled Rubiales's actions "inappropriate and unacceptable".
One day before Vilda condemned the president's actions, his entire coaching staff resigned in protest against Rubiales, while 81 women's players plan to boycott matches until he is removed from power.
The Spanish Football Federation is currently under the control of acting president Pedro Rocha, who has admitted that he is "ashamed" by Rubiales's behaviour, and the chief has also relieved Vilda of his duties after a highly controversial tenure.
Despite last year's mutiny, the RFEF paid tribute to Vilda for his "impeccable personal and sporting conduct", saying in a statement: "The Royal Spanish Football Federation, in one of the first renewal measures announced by President Pedro Rocha, has decided to part ways with Jorge Vilda's services as the sports director and head coach of the women's national team.
"The RFEF appreciates his work leading the national team and his role as the highest sports authority for the women's teams, as well as the successes achieved during his tenure, culminating in the recent World Cup victory.
"We highly value his impeccable personal and sporting conduct, as he has been a key figure in the significant growth of women's football in Spain. Throughout his extensive tenure, Vilda has been a promoter of respect and sportsmanship values in football.
"The RFEF wants to express its gratitude to Jorge Vilda for his services, professionalism, and dedication over all these years, wishing him the best success in the future. The RFEF inherits an extraordinary sporting legacy thanks to the implementation of a recognized playing style and a methodology that has driven growth for all women's national team categories."
Vilda departs with a record of 75 wins from 108 games as Spain head coach and has been replaced by Montserrat Tome, a former Barcelona Femeni midfielder and four-cap Spain international.
The world champions are due to return to action with a pair of Nations League fixtures against Sweden and Switzerland on September 22 and 26 respectively.