Marc Janko scored in the 33rd minute after lax defensive marking, and the United States ended a record-setting year with a 1-0 loss to Austria.
Hungarian referee Istan Vad failed to allow a goal for the United States when Geoff Cameron's header off Michael Bradley's corner kick appeared to cross the goal line in the 17th minute before it was swatted away by goalkeeper Robert Almer.
Janko's goal, started by David Alaba's attacking move, ended a 453-minute shutout streak in international and club play for Howard, Everton's starter.
The U.S. finished the year with a team-record 16 victories and qualified for its seventh straight World Cup. Austria failed to qualify for next year's tournament in Brazil.