The U.S won Friday's match 1-0 in Denver but Costa Rica were furious about the conditions, saying the pitch markings were not visible, the ball could not be passed properly and stadium employees entered the field while the ball was still in play to clear away snow.
"FIFA has examined the content of the letter and... has confirmed that the conditions established in the regulations for an official protest have not been met by the Costa Rica FA," said football's governing body in a statement.
"Therefore, the result of the match played on 22 March stands and is considered as valid."
2014 World Cup rules states that protests about the pitch and markings must be made in writing to the referee before the start of the game by the head of the delegation.
If the pitch becomes unplayable during the match, the team captain must lodge a protest with the referee in the presence of the opposing captain, and this must be confirmed in writing within two hours of the end of the game.
Costa Rica coach Jorge Luis Pinto said the match was an "embarrassment to football" after the game and the country's football federation said later that the conditions were a threat to the "physical integrity" of the players.
The episode has already led to speculation that the U.S could face a hostile reception in the return fixture.
Costa Rica could retaliate by staging the return fixture in the Saprissa stadium, an small but intimating venue where the fans are close to the pitch, rather than the new National Stadium, which has a running track around the field.
The defeat left Costa Rica bottom of the six-team final stage in the CONCACAF region qualifiers with one point from two games.
