The first game of the Saturday doubleheader proved decisive in determining which teams would progress, as Nicaragua - the other side that came into the day with a chance to qualify - fell to El Salvador.
The team led by head coach Luis Londoño knew that it had to win to maintain any chance of advancing and took the lead through Yader Bonilla in the 13th minute off an assist from Eudis Gutierrez.
Julio Cesar Amaya, however, continued his excellent form at the tournament for El Salvador, replying from distance midway through the first half to level the score. Juan Barahona then put the Cuscatlecos ahead just prior to the break with another shot from outside the area.
Second-half substitute Daniel Melgar scored what proved to be the game-winning goal for the Salvadorans in the 69th minute; his first of the competition.
Bonilla completed his brace for Nicaragua in the 74th minute, but the definitive 3-2 scoreline favored neither team as both were eliminated.
In the afternoon match, Costa Rica defeated host Guatemala, 2-0, with the pair already assured of places in next year's confederation finals.
Berny Burke put the visitors in front 1-0 in 17th minute. And just before the stroke of halftime, Randal Leal doubled the Ticos' advantage, which they would not surrender.
After a full week of action at the Estadio Julio Armando Cobar, Honduras came out on top of the table with an impressive 13 points from five games. Costa Rica and Guatemala followed in second and third, respectively.
The Central American trio will join host Panama, Barbados, Cuba, Haiti, Jamaica and Trinidad & Tobago, plus automatic North American qualifiers Canada, Mexico and the United States, at the CONCACAF Under-17 Championship, which will be played April 6-19.