The victory also came as a huge morale boost for the Americans ahead of the FIFA Confederations Cup.
USA lie in Group B along with Egypt, Italy and Brazil in the global competition that gets underway on June 24th.
Visitors Honduras took an early lead when Carlo Costly opened the scoring only four minutes after the kickoff.
Landon Donovan brought the score level after converting a spot kick two minutes from the interval.
Carlos Bocanegra put USA ahead with a nice diving header nine minutes after the hour mark.
Bob Bradley's men were in dire need to win this game, after losing to Cost Rica 3-1 in their previous qualifier.
After claiming all three points, USA cemented their place in second spot with 10 points.
The first three countries of the six-team group will directly reach the World Cup by the end of the qualifiers.
The fourth-placed side will face the fifth-placed team of the South American qualifying stage in a playoff.
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