After investigating the incident from the quarter-final, won 2-1 by Brazil, FIFA's Disciplinary Committee has ruled that no retrospective action could be taken.
In a statement, soccer's world governing body said their own rules prevented them reopening the case because the incident had already been dealt with by the referee on the pitch.
"After an analysis of the matter and the extensive submission and documentation received from the CBF (Brazilian Football Confederation), 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 (FDC) for the Disciplinary Committee to be able to intervene in such a situation," the statement read.
"In particular, in this specific case, no retrospective action can be taken by the FIFA Disciplinary Committee, since the incident involving the Colombian player Juan Camilo Zuniga Mosquera did not escape the match officials..."
FIFA also said it could not consider Brazil's appeal against captain Thiago Silva's yellow card that will keep him out of Tuesday's World Cup semi-final against Germany. The governing body said there was "no legal basis" to grant such a request.
The defender was booked against Colombia for blocking keeper David Ospina as he was taking a kick, and as it was his second of the tournament he was automatically suspended.
NEYMAR DISAPPOINTMENT
FIFA, in a break from its standard formal statements, expressed its disappointment that Neymar - one of the host nation's most popular and charismatic players - had been ruled out of the World Cup because of the injury.
But FIFA said the extent of the injury and the profile of the player involved could not have any bearing on their disciplinary rules.
"It is important to note that 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," FIFA said.
"Finally, as a general remark, FIFA and the FIFA Disciplinary Committee regret any incidents occurring on the pitch that in particular have a negative impact on the health of players.
"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."
Neymar's premature exit from the World Cup has provoked a mixture of shock and anger in the samba nation.
Brazilian television stations interrupted their normal programming on the weekend to broadcast live shots of Neymar leaving the team's training base on a helicopter while Brazil President Dilma Rousseff sent the injured player a letter.
The initial shock over Neymar's injury quickly turned to fury as the collision with Zuniga was further scrutinised.
Neymar was carried off the field in tears, and later diagnosed with a fractured vertebra, when Zuniga came rushing in from behind and kneed the Brazilian striker in the back.
Zuniga was not booked over the incident and sent a personal note to Neymar explaining that it was an accident but not everyone agreed with his version of events with former Brazil striker Ronaldo calling it an "evil" tackle.
