Alvaro Sanchez, Pablo Herrera and Roberto Segura scored for the Ticos, who had soundly beaten Panama, 3-0, in the opening game of the three-team Group B on Friday.
Panama will need to beat Guatemala on Tuesday to advance to the semifinals.
Honduras got goals from Mario Rodriguez, former MLS player Saul Martinez and Walter Martinez, who has being mentioned as a possible D.C. United addition, as well as an own goal in the win over Nicaragua that ensured the Catrachos of their fourth straight trip to the Gold Cup.
The four semifinalists and the winner of the fifth-place game move on to the Concacaf championship.
El Salvador recovered from its 1-1 tie with Nicaragua to beat Belize, 4-1, and claim the second spot from Group A in the semifinals.Alfredo Pacheco scored twice from the penalty spot in the first half hour.