Johnny Acosta headed Costa Rica to an early lead before Celso Borges made it two goals within the first 10 minutes.
In the shadows of half-time, Clint Dempsey's penalty restored hope for the Americans but Costa Rica's Joel Campbell finished off the game 15 minutes from time, while the USA ended the game with 10 men following Matt Besler's second yellow card.
It was a dynamic start from the Costa Ricans, who should have opened the scoring through Bryan Ruiz on two minutes, only seconds before Acosta headed home Campbell's quality corner.
DaMarcus Beasley tried valiantly to clear the goal-bound header on the post but only succeeded in deflecting it into the net.
Bryan Oviedo was troubling the USA from wide positions and after creating an opportunity headed over the bar by on-loan Arsenal striker Campbell, the Everton winger floated a cross into the box in the 10th minute that was met by Borges and powered past goalkeeper Tim Howard.
The USA finally managed to get some possession after Borges' goal and had two long-range shots from Jermaine Jones and Fabian Johnson that perked Costa Rican goalkeeper Keilor Navas' interest.
Just before half-time, the USA managed to pull a goal back after Johnson was brought down in the area by Navas.
Former Tottenham midfielder Dempsey stepped up to score the penalty home despite Navas getting a hand to the ball.
Costa Rica retreated into their shell in the second-half, attempting to absorb the USA pressure and spring their own attacks quickly on the break.
This tactic worked as Campbell found himself through on goal, kept his composure and rolled the ball past Howard to re-establish the two-goal lead.
Adding to the loss, USA defender Besler was sent off for a second bookable offence 10 minutes from time.
With Costa Rica climbing to the top of the standings, the USA is one-point behind the leaders but hold a one-win advantage over Honduras, who are in the last automatic qualification position.
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