Altidore's 73rd-minute goal was the difference between the teams at Rio Tinto Stadium as the home side were rewarded for their domination to complete a trio of June fixtures with a 100 per cent record after wins over Jamaica and Panama.
The U.S head the six-team group on 13 points from six matches with the top three qualifying automatically for Brazil and the fourth-placed side, currently Honduras on seven points, facing New Zealand in a two-legged play-off for a finals spot.
The U.S started slowly in the final round of matches before climbing to the top of the standings on the back of four wins and a draw, with the latest triumph representing a semblance of revenge after Honduras won the reverse fixture 2-1 in February.
Altidore settled the contest with his fourth goal in as many matches when he controlled a cross from Fabian Johnson and guided the ball past Honduran goalkeeper Noel Valladares.
The visitors arrived in Utah weakened by injury and through the loss of influential defender Victor Bernardez and midfielder Luis Garrido after both picked up suspensions for cautions in the 2-0 win over Jamaica last week.
As a result, the U.S dominated possession and restricted the Hondurans to just a single shot on goal despite the enforced absence of DaMarcus Beasley, who was also suspended for the tie.
U.S coach Jürgen Klinsmann had little to fear from the visitors as his side extended their unbeaten home record in qualifiers to 25 games but he can expect a much tougher test on September 6 with a daunting trip to second-placed Costa Rica.
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