Striker Alvaro Saborio set the Ticos on their way on the Saprissa stadium's frayed artificial pitch in the first minute with a 25-metre shot which dipped over goalkeeper Tim Howard.
The hosts doubled their lead before the quarter-hour mark when a sweeping move down the left ended with Celso Borges side-footing the ball into an empty net.
The U.S., unbeaten in their opening three games in the group, never looked like finding a way back and nearly went further behind when Howard tipped away Saborio's header.
With Costa Rica being roared on by a crowd of 20,000 Saborio had another chance before halftime but fired his snapshot over the bar.
Substitute Pablo Herrera buried the visitors in the 69th minute when he collected the ball nearly the touchline, twisted past his marker and beat Howard at his near post.
Howard saved the U.S. from further humiliation late in the game when he turned away Walter Centeno's well-struck free kick.
Landon Donovan pulled one back with an injury-time penalty to give the scoreline a tinge of respectability.
Costa Rica, attempting to qualify for their third successive World Cup, top the six-team group with nine points from four games, two ahead of their opponents.
