The victory boosted the Hondurans into the final-round lead with three points, pending the outcome of the Mexico-Jamaica and Panama-Costa Rica matches later in the day.
It was the first time in five World Cup qualifiers that Los Catrachos on their own soil defeated the Americans, snapping a four-game home winless streak (0 wins, 1 draw, 3 losses) against their northern visitors.
It also was the first time the U.S. lost the opening game of the hexagonal round.
The absence of midfielder-forward Landon Donovan, who has taken some time off from soccer, definitely impacted the American attack, which was sporadic, at best.
"There were too many mistakes and too many players today just didn't reach their usual potential," U.S. coach Jurgen Klinsmann said. "It is really difficult to come away with a win here if you do not have everybody 100 percent at their limits."
Bengtson, who plays for the New England Revolution in the USA's Major League Soccer, broke a 1-1 deadlock amid confusion on the U.S. backline. Oscar Boniek Garcia beat Geoff Cameron on the right side of the penalty area and sent a short pass to Bengston, who beat his man, Omar Gonzalez, as he connected from six yards past goalkeeper Tim Howard at the Estadio Olimpico Metropolitano.
"It was individual mistakes that happened," Klinsmann said. "We had problems closing down the passing lanes."
The U.S. had one last gasp four minutes into stoppage time as Gonzalez headed a corner kick over the crossbar just before fulltime was called.
It was a deserved win for Los Catrachos, who played a spirited game, finding holes in the U.S. defense.
The Hondurans enjoyed the territorial advantage in the opening minutes in the game, played in 84-degree heat. Garcia, who plies his trade with the Houston Dynamo (MLS), sent a shot wide left in the second minute, before Mario Martinez (Seattle Sounders) fired a shot that looked more like a cross that U.S. goalkeeper Tim Howard was able to hold two minutes later.
Martinez tried a long-range attempt in the 22nd minute, but that effort sailed wide left.
Eddie Johnson created the Americans' early chances. Geoff Cameron headed his 18th-minute corner kick over the crossbar and Jozy Altidore kicked a Johnson feed wide right in the 29th minute.
Midfielder Roger Espinoza made the U.S. sweat as he found some room down the left side, penetrated into the penalty area and sent a short pass to Arnold Peralta that defender Fabian Johnson managed to clear out of harm's way in the 31st minute.
Two minutes later, Espinoza was at it again. This time he launched a 19-yard blast that Howard parried out of bounds for a corner kick.
The U.S. found the range in the 36th minute. Altidore sent the ball back to midfielder Jermaine Jones, who blooped a pass to an onrushing Clint Dempsey on the right side in the penalty area. Dempsey then volleyed the ball past goalkeeper Noel Valladares to the upper left side for his 31st international goal and a 1-0 lead.
The Hondurans did not take long to equalize as Juan Carlos Garcia scored off a bicycle kick four minutes later. After Gonzalez cleared the ball over the goal line, a Honduran corner kick bounded through the penalty area. Victor Bernardez ran the ball down and sent it into the middle of the box to Maynor Figueroa. Garcia gained possession and scored a spectacular goal to knot the score at 1-1 in the 40th minute.
After a giveaway by midfielder Michael Bradley, the Hondurans broke quickly and thought they had taken the lead in the 56th minute, but forward Carlo Costly was called offside.
Garcia demonstrated that he could play some defense as well in the 65th minute as he managed to deflect Dempsey's shot from the right side.
Klinsmann made three second-half substitutions, including replacing midfielder Danny Williams with Maurice Edu in the 58th minute.
"Things kind of calmed down a bit," he said. "He cleaned more up. He played simple balls. We kept more possession. That's what we were asking for."
The U.S., which plays three of its first four qualifiers on the road, will face Costa Rica in its first hexagonal home game in Commerce City, Colo. on March 22, while the Hondurans remain at home to welcome Mexico the same day.