The result means the U.S. remain in third place in the six-team qualifying group ahead of Honduras only on goal difference.
Both the United States and Honduras, who beat Trinidad and Tobago 2-1, have just eight points from seven games.
The top three teams in the group qualify automatically for Russia and the fourth-placed side goes into a playoff with a team from Asia.
Following the U.S. defeat, Mexico sealed their ticket to Russia with a 1-0 win over Panama in Mexico City.
“We still have three games left in the competition and we're still in position to qualify for the World Cup,” U.S. coach Bruce Arena said before the Mexico result.
"Mexico and Costa Rica are (basically) qualified.
“It’s going to be a fight between the other four teams for that remaining spot.
Costa Rica were superior throughout and took the lead after half an hour when captain Bryan Ruiz slipped a nice through ball to Urena, who evaded defender Tim Ream to angle the ball past keeper Tim Howard from just outside the six-yard box.
The U.S. improved slightly at the start of the second half but lacked a cutting edge against a team that was content to keep possession and frustrate the home side.
Keylor Navas made one superb reflex save from an otherwise subdued Christian Pulisic and he also blocked a Jozy Altidore shot with 10 minutes remaining.
But Urena completed the win just seconds later when he ran through another gaping hole in the U.S. defence to give Howard no chance from 15 yards out.
The win moved Costa Rica on to 14 points and they now sit three points behind leaders Mexico.
Behind the top two, there is a dogfight, with only one point separating the U.S., Honduras and Panama.
Honduras brought themselves back into contention with a vital away win.
Alexander Lopez and Alberth Elis scored first half goals for the Central Americans and although Joevin Jones got one back from the penalty spot midway through the second half, the Hondurans held on to take all three points.
(Reporting by Andrew Downie; Editing by Greg Stutchbury / Ian Ransom)
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