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."
Neymar's best and worst moments of the 2014 World Cup
Neymar's best and worst moments of the 2014 World Cup
1/9 Neymar scores his first against Croatia
After going a goal behind in the very first match of the tournament courtesy of a Marcelo own goal, Neymar got his tally off the mark as he scored from long range to drag Brazil level.
2/9 He adds his second in controversial circumstances
Despite a stop-start, jerky run up, Neymar converts from the penalty spot to give Brazil the lead and they would go on to secure a 3-1 victory. However, the Croatians were infuriated by what they perceived as a dive from striker Fred to win the penalty. Not that it mattered to Neymar, who duly took his chance from the spot.
3/9 But was he lucky to be on the pitch?
A stray elbow on Luka Modric could have warranted a red card for Neymar, but he escaped with a yellow and was on hand to score later in the match when the opportunity arose.
4/9 Tears of pride
Neymar in tears during the Brazil national anthem before the game with Mexico, such is the importance of the occasion
5/9 Neymar left frustrated against Mexico
An unimpressive Brazil side were left hugely frustrated by Mexico goalkeeper Guillermo Ochoa. In a man-of-the-match display, Ochoa kept out a close range header from Neymar to see the match end as a goalless draw.
6/9 Back on form and back in the goals
You can’t keep a quality player quiet for long though, and unfortunately for Cameroon, their dismal World Cup campaign came to an end at the hands of another Neymar brace. Taking his tally to four goals, Neymar put himself in the reckoning for the Golden Boot, although his injury has put paid to that dream for now.
7/9 Caught with his pants down
Despite being the poster boy of Fifa’s World Cup, the governing body confirmed that they were investigating Neymar for allegedly breaching sponsorship rules by partially showing the top of his underwear that may or may not have been part of a sponsorship stunt. Eventually, Fifa conformed they would take no further action.
8/9 Neymar’s penalty prowess sees off Chile
After a hard-fought 120 minutes, Brazil and Chile were locked at 1-1 courtesy of David Luiz and Alexis Sanchez strikes. Mauricio Pinilla and Sanchez both saw their penalty shootout efforts saved by Julio Cesar, but Willian and Hulk followed suit. With the weight of a nation on his shoulders, Neymar coolly slotted home from the spot, which turned out to be the match-winner as Gonzalo Jara then hit the post to send Brazil through to the quarter-finals.
9/9 One assist, no goals and a trip to hospital sees Neymar done
The forward had seen his impact in the quarter-final against Colombia somewhat limited due to the rough and tumble nature of the match – although the Brazilians were just as guilty of using the tactic against James Rodriguez. His corner allowed Thiago Silva to bundle the ball across the line for the opener, before Juan Camilo Zuniga’s ill-timed knee in the back cracked on of Neymar’s vertebrae and ended his run at this year’s World Cup.
The decision will infuriate hosts Brazil - their 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.