Jorge Vilda (right) is considered a close ally of Luis Rubiales (left)
Montse Tome has been named as his successor, becoming the first woman to hold the position.
Spain's win was overshadowed by the country's football federation president Rubiales kissing forward Jenni Hermoso, which she said was not consensual.
Most of Vilda's coaching staff resigned and 81 players refused to play for Spain in the aftermath.
Rubiales has refused to resign but has been provisionally suspended by Fifa, football's world governing body.
In a statement, Spanish federation the RFEF did not give a specific reason for Vilda's dismissal, saying he had been "a promoter of the values of respect and sportsmanship in football".
However, the RFEF has been exploring whether it could sack 42-year-old Vilda - considered a close ally of Rubiales - since last week.
The RFEF called the move "one of the first renewal measures" announced by interim president Pedro Rocha, who has taken on the role while Rubiales is suspended by Fifa.
Vilda was spotted applauding Rubiales at the RFEF's extraordinary general assembly earlier in August - when Rubiales repeatedly insisted he would not resign and said he would offer Vilda a new deal - though he has since criticised his behaviour.
"The RFEF appreciates [Vilda's] work at the head of the national team and in his functions as the head of sports for the women's teams, as well as the successes achieved during his time crowned with the recent achievement of the World Cup," said the RFEF.
"We value his impeccable personal and sporting conduct, being a key piece in the notable growth of women's football in Spain."
-- Courtesy of BBC Sport