A group of around 50 fans called for the resignation of CBF president Ricardo Teixiera, who many Brazilians blame for the crisis which has hit the sport in their country including the once mighty national team itself.
They changed various slogans of which "Get out, Teixeira," was the most polite and launched black balloons into the air as a sign of mourning for Brazilian football.
Monday's 2-0 defeat by the Central Americans in their quarter-final Copa America tie in Colombia was the latest setback for Brazil, following recent defeats against Ecuador, Australia and Uruguay and draws with Canada and Japan.
Brazil, the only country to have played at all 16 World Cups, are also in danger of losing their proud record after slumping to fourth place in the South American World Cup qualifying group.
Brazil cannot afford any more slip-ups as the top four teams qualify automatically for Japan and South Korea and they are only ahead of Uruguay on goal difference. Their next match is at home to Paraguay in mid-August.
The CBF are blamed for most of the problems faced by the team.
Earlier this year, a Congressional inquiry into Brazilian football produced a 700-page report condemning the CBF's administration and pointing a number of irregularities.
It accused Teixeira of committing 13 criminal offences as well as breaking CBF statutes which banned him from receiving a salary from the organisation.
Angry football supporters wearing red noses protested outside headquarters of the Brazilian Football Confederation (CBF) on Tuesday after the four-times world champions' shock defeat by Honduras the day before.
