Thiago Silva will be suspended for Brazil's World Cup semi-final against Germany - and FIFA has also ruled out action by its disciplinary committee for the challenge by Colombia's Juan Zuniga which left Neymar with a serious injury.
Brazil's federation, the CBF, had appealed against Thiago's yellow card but FIFA's disciplinary committee refused to consider it - appeals against cautions are only permitted in exceptional circumstances.
A FIFA statement said: "The disciplinary committee... cannot consider the matter given the fact that there is no legal basis entitling it to grant such request."
The CBF had also pushed for action against Zuniga but this was rejected by FIFA's disciplinary committee who said the referee had seen the incident.
FIFA added: "After an analysis of the matter and the extensive submission and documentation received from the CBF, the chairman came to the conclusion that the FIFA disciplinary committee cannot consider this matter in light of the conditions outlined in the FIFA disciplinary code... to be able to intervene in such a situation."
The decision will infuriate hosts Brazil, whose coach Luiz Felipe Scolari claimed Colombia had been "hunting" Neymar, who suffered a fractured vertebra when Zuniga caught him in the back with his knee.
The FIFA statement said disciplinary committee chairman Claudio Sulser had deep sympathy for Neymar but that regulations meant retrospective action could not be taken in this case.
The statement said: "The chairman of the FIFA disciplinary committee deeply regrets the incident and the serious consequences on Neymar's health.
"No retrospective action can be taken... since the incident involving the Colombian player Juan Camilo Zuniga Mosquera did not escape the match officials' attention.
"The conditions by which the FIFA disciplinary committee can intervene in any incident have to be considered independently of the consequences of that incident, such as an unfortunate injury suffered by a player.
"We wish Neymar a prompt and complete recovery as we wish the same for all players who have sadly been ruled out of the World Cup through injury."
Thiago picked up the caution against Colombia, imposed after he blocked goalkeeper David Ospina taking a kick, and as it was his second of the tournament he was automatically suspended.
Appeals against yellow cards are only allowed in exceptional circumstances, such as cases of mistaken identity, and overturning would have been hugely controversial and would have allowed other teams to claim that the governing body was favouring the hosts.
In an infamous past incident, FIFA allowed Garrincha to play in the 1962 World Cup final despite the Brazilian forward being sent off in the semi-final.