Panama and Canada won through at the Panama City-based tournament on Saturday.
Sunday’s early match produced a stunning upset as USA were denied a berth at the FIFA U-17 World Cup for the first time.
Scores were level 1-1 at half-time with Alberth Elis and Kevin Alvarez extending their margin to 3-1 as Honduras reached just their third FIFA U-17 World Cup.
USA is the only country to have participated in every FIFA U-17 World Cup, having qualified a record 14 times.
The 2005 and 2011 world champions will now feature on the world stage for the eleventh time.