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 percent record after wins over Jamaica and Panama.
The US 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 berth.
The US 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 US 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.
US coach Juergen 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.
Bryan Ruiz and Celso Borges scored second-half goals as Costa Rica earned a 2-0 win against Panama on Tuesday to maintain their hold on a place for an automatic qualifying place for next year's 2014 World Cup finals.
The United States, who beat Honduras 1-0 earlier on Tuesday, lead the six-team group in the final round of qualifying from North, Central America and the Caribbean (CONCACAF) on 13 points from six games.
Costa Rica have 11 points from six matches while Mexico are in the third and final automatic place with eight points from six games.
The fourth-placed team, currently Honduras on seven points, meet Oceania winners New Zealand for a further place in the finals in Brazil.
In a rain-swept National Stadium in San Jose, Ruiz opened the scoring in the 47th minute from a free kick before Borges produced a long-range strike to double the advantage four minutes later.
Panama's Blas Perez returned from a stomach virus that had sidelined him but could not get the attack on track for the visitors.