The Qatari FA had said the German-based trio of Ailton, Dede and Leandro would be given citizenship within a week.
But Fifa's emergency committee ruled on Wednesday that players must have a "clear connection to that country" if they wanted to play for another nation.
The rules now state a player must either have lived in a country for at least two years, or have a parent or grandparent who was born there.
"Naturalization that allows players with no obvious connection to the new country to play for that country's national teams is not the aim and object of the (Fifa) statutes," said Fifa president Sepp Blatter.
Fifa's rules state a player who has never competed at international level can switch to another country if he is granted citizenship.
Qatar national manager Phillipe Troussier - the Frenchman who coached Japan in the last World Cup - has been trying to naturalize overseas players discarded by their national teams.
None of the Brazilian trio have made any full international appearances for Brazil and none have any previous connections with the Gulf state.
Ailton has reportedly been offered more than 1m euros to play for Qatar, but the Bundesliga's current top scorer denied he is a mercenary.
"Money is not the decisive factor here as I earn good money at Werder Bremen," he said.
"If Brazil ignore me for 2006, then I have to find another way to get there."
Former Kenyan athlete Stephen Cherono switched allegiance to Qatar and won the World Championship gold medal for them in the 3000m steeplechase under the name of Seif Saeed Shaheen.
Blatter said he would raise the issue with the Fifa Congress, meeting in Paris in May, with a view to changing the statutes.
