The victory ensured Honduras of a fourth straight trip to the CONCACAF Gold Cup and a ninth appearance in 10 tries.
El Salvador edged closer to a fourth appearance in its last five tries in the Gold Cup with a 4-1 victory over Belize earlier Saturday. The results left Honduras atop Group A with six points, two ahead of El Salvador with the two set to face off Monday night in the first-round finale.
Nicaragua is third with one point, just ahead of Belize. The top two advance to the semifinals of the Copa de Naciones Digicel de UNCAF while the third-place team will earn a playoff for fifth place and the last berth in the 12-team Gold Cup field.
An own-goal by David Solorzano gave Honduras a 2-1 lead in the 65th minute, and Saul Martinez and Walter Martinez added goals in the final 17 minutes to complete the victory.
Playing without captain Amado Guevara, who was suspended after being red carded in second-half injury time of Thursday's 2-1 victory over Belize, Honduras led on Mario Rodriguez's goal in the 16th minute. But Armando Reyes equalized in the 30th for Nicaragua, which is seeking its first trip to the Gold Cup.
In the earlier game, Alfredo Pacheco converted a pair of penalties in the first 30 minutes and El Salvador recovered from its opening 1-1 draw against Nicaragua on Thursday.
Jeromy James pulled Belize within a goal in the 73rd, but Ramon Sanchez restored the two-goal advantage two minutes later and Carlos Ayala added insurance in the 88th.
Costa Rica was in position to claim a semifinal berth and a seventh straight place in the Gold Cup with a draw Sunday against Guatemala.
