Carlos Pavon scored for Honduras in the 19th and 27th minutes, Amado Guevara in the 61st and David Suazo in the 82nd minutes, while Kerry Baptiste scored five minutes from time for Trinidad and Tobago, whose slim hopes of reaching next year's finals in South Africa have dwindled even further.
Honduras came into the match buoyed by their 4-0 victory over Costa Rica on 12 August.
Trinidad and Tobago had beaten El Salvador 1-0 on the same night and hoped to gain a bit more breathing room in the six-nation final round of qualifying in the region, from which three teams advance directly to the FIFA World Cup finals. The fourth-placed team plays off for a berth against the fifth-placed team from South America.
The victory gave Honduras 13 points, level with USA but ahead on goal difference. Trinidad and Tobago and El Salvador, who fell 2-1 to USA earlier, both have five points and are all but eliminated from contention.