Ricardo Teixeira stood down as head of the Brazilian Football Federation and the 2014 World Cup organising committee on health grounds.
He announced over the weekend he would be taking a leave of absence due to his health and on Monday confirmed his departure was permanent.
A statement read: 'I leave the presidency of the CBF (national federation) permanently with the sense of mission accomplished.
'It's not easy to preside passion. Football in our country is associated with two things: talent and disorganisation.
'When we win, talent is praised. When we lose, it's about disorganisation.
'I did what was within my reach, sacrificing my health. I was criticised in the losses and undervalued in the victories.'
Teixeira has had moments of controversy during his leadership of the CBF but can also point to the highlight of two World Cup victories, in 1994 and 2002.
Just last week there was speculation he would stand down due to accusations of impropriety but state federations voted unanimously for him to stay.
In 2001, the Brazilian Congress investigated Teixeira on suspicion of 13 crimes, including tax evasion, money laundering and misleading lawmakers, but no charges were brought.
He has also been investigated for allegedly taking kickbacks from a marketing firm that worked closely with FIFA in the 1990s.
He denied all the allegations and has never been convicted of any offence.
Teixeira also came under fire from FIFA last week with secretary general Jerome Valcke expressing his concern over the lack of progress on preparations for the 2014 World Cup.
Valcke said Brazilian organisers needed a kick up the backside - a comment which led to the country's government saying they no longer wanted to deal with him.
Brazil's sports minister Aldo Rebelo said Valcke's comments were 'unacceptable' and inaccurate.
