Canavan, 19, started the match at the Estadio Municipal de Agueda.
Abel Camara and Josue scored the late goals to seal the win for the home side.
Scunthorpe's recent signing Ramon Nunez watched from the bench as Honduras endured a miserable start to life in his first international under new coach Luis Fernando Suarez.
The South American side were comfortably beaten 4-0 by South Korea in a friendly in Seoul. He is likely to feature on Tuesday night against China.