Roy Millers' 25th minute header, after Honduras keeper Noel Valladares parried out a Celso Borges free-kick, was enough to give Costa Rica a 1-0 victory in San Jose which moved them to the top spot.
Costa Rica (seven points) lead on goal difference from the United States (seven) while Mexico also have seven points although they have played one more game.
Panama (6), Honduras (4) and Jamaica (2) complete the bottom half.
The United States were lucky to be part of the leading trio after Brad Evans struck in injury time to give Juergen Klinsmann's team a 2-1 win in Kingston against Jamaica.
Jermain Beckford's 89th minute header looked to have earned Jamaica a point after the United States had led through a Jozy Altidore goal on the half hour.
But Michael Bradley slipped the ball inside the area to Evans who, with a surprising amount of space, drove past Jamaican keeper Donovan Ricketts to seal the win.
It wasn't an entirely convincing performance from the US but Klinsmann was pleased with the character his team showed as they responded to the blow of a late equaliser to get their first ever win in Kingston in a qualifier.
"They were angry with themselves about allowing that goal and they responded," said the former German national team striker and coach.
Klinsmann's team started brightly and went close to an opener in the second minute when Bradley struck the post with a drive from 20 yards out.
The United States took the lead when Altidore, who had an early effort ruled out for offside, rose to power in a superb cross from winger Graham Zusi.
Nine minutes later Jamaica almost drew level when Rodolph Austin burst through on to a Ryan Johnson pass but his low shot struck the post.
The United States looked in charge but with a minute of regulation time remaining, Beckford was left unmarked to head home from an Austin cross.
However, there was more drama to come and three minutes later the United States restored their advantage to get their first away win in qualifying.
There were some other major positives for Klinsmann as Evans looked at ease in a new role at right-back, Zusi played with intelligence on the right flank and Altidore, who scored in Sunday's 4-3 friendly win over Germany, looked to be full of confidence.
Mexico will be disappointed with their fourth draw in five games but Panama are proving to be the surprise package in the group.
Surprisingly Mexican striker Aldo Di Nigris, who scored in Tuesday's 1-0 win in Jamaica, was left on the bench and did not enter until he replaced the injured Javier Hernandez in the 80th minute.
There were few chances but Panama went the closest in the second half when, from a corner, striker Blas Perez fired through the crowded penalty area but Mexico keeper Jesus Corona got down well.
Panama, who have never reached a World Cup finals, travel to Seattle on Tuesday to face the United States.
Mexico host Costa Rica while Jamaica travel to Honduras.