Growing frustrated of limited opportunities at Manchester United, Hernandez signed a season-long loan at Real Madrid.
But the striker has been restricted to just 52 minutes of game time since joining the European champions, with all three of his appearances coming off the bench.
Hernandez gave Escober no chance with a fantastic shot across him but the keeper will have been furious with his defence after Mexico's second goal.
Alanis' free header will have caused serious concerns for Honduras coach Hernan Medford, but they improved after the break.
But despite enjoying good spells of possession, Honduras could find no way back into the contest as Mexico recorded their second win in a row and a third consecutive clean sheet.
Miguel Herrera's side next play Panama on Sunday, while Honduras face a tough assignment against United States two days later.
