Scolari promised to win the tournament at home, but Brazil was eliminated in the semifinals by a disastrous 7-1 loss to eventual champion Germany that matched the national team's worst defeat in its 100-year history. Brazil also lost 3-0 to the Netherlands in the third-place match.
Scolari's contract ended after the World Cup and he handed over the command of the team after Saturday's match, saying it would be up to the confederation to decide whether he would remain at the helm of the five-time world champions.
In a statement, the confederation said President Jose Maria Marin accepted what it called "Scolari's resignation."
"Scolari and his staff deserve our respect and our gratitude," the statement said. "They were responsible for making the Brazilian people regain their love for the Selecao even though we did not reach our greater goal (of winning the title)."
Scolari's replacement was not immediately announced. Assistant Carlos Alberto Parreira, the coach who led Brazil to the 1994 World Cup title, was also leaving.
The confederation said Marin would give further explanations in a news conference on Thursday.
Scolari, who led Brazil to the 2002 World Cup title, had said after Brazil's loss to the Netherlands that he would turn in a report of his work with the national team and Marin would then analyze what he would like to do.
Scolari publicly apologized to fans after the loss to Germany, saying he knows it will never be forgotten, and defended his work with Brazil since returning in late 2012. In 29 matches, he led the nation to 19 wins, six draws and four losses. Brazil won last year's Confederations Cup, the World Cup warm-up tournament.
"I don't think you can analyze the entire work based on only one disastrous result," Scolari said after Brazil's loss to the Dutch. "I think the job was well done."
The once-popular coach was loudly booed by fans after Brazil ended the home tournament on Saturday. Despite high expectations, Brazil struggled throughout the competition, finishing with three wins, two draws and two losses.
Scolari had been betting on young striker Neymar to carry the team to the title, but he was shelved by a back injury in the quarterfinals.
Scolari was picked to lead the 2014 team mostly because of his popularity and experience from the 2002 title, but many critics said he was outdated as a coach. Before rejoining the national team, Scolari was coming off relegation in the Brazilian league with traditional club Palmeiras.
Among those touted to replace Scolari are Tite and Muricy Ramalho, who have been successful with local clubs in recent years. Ramalho is a four-time Brazilian champion, while Tite led popular Corinthians to the Club World Cup title in 2012. There is also talk in local media about international coaches, including Pep Guardiola, Jose Mourinho, and Chile's Argentine coach Jorge Sampaoli.
Brazil's next official tournament is the 2015 Copa America. The team is expected to play four friendlies this year, the first one against Colombia on Sept. 5 in Miami. It will also play Ecuador on Sept. 8 in New York, Argentina on Oct. 11 in Beijing and Turkey on Nov. 12 in Istanbul.
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