Luis Fernando Suarez's men needed just a point in the final round of fixtures to guarantee their progress alongside the United States and Costa Rica although they were made to work hard by a home side that finished the campaign without a win.
Carlo Costly put Honduras ahead in the opening minute, only for Je-Vaughn Watson to equalise almost straight away.
Maynor Figueroa gave Honduras the lead once more with a 31st-minute free-kick that deflected off the wall but Rodolph Austin netted a penalty just before the hour mark.
The visitors held on in the final half hour to ensure their progress to Brazil 2014, the third time they have qualified for the World Cup following on from 1982 and 2010.
In the event, their result in Kingston did not matter as Mexico suffered a 2-1 defeat in Costa Rica.
Goals from Fulham striker Bryan Ruiz and Alvaro Saborio in-between Oribe Peralta's leveller ensured Costa Rica finished their campaign with a flourish as they finished behind only the USA, who hit back to defeat Panama 3-2 and help Mexico finish fourth in the standings.
Panama looked set to leap above Victor Manuel Vucetich's men and set up a play-off clash with New Zealand after taking a 2-1 lead in Panama City thanks to goals from Gabriel Torres and Luis Tejada - in-between Michael Orozco's equaliser for the USA.
However, two injury-time goals from Graham Zusi and Aron Johannsson turned the game in the visitors' favour as Mexico were given a lifeline.