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.
That at least ensured he was fresh heading into this clash and the forward fired Mexico superbly in the 22nd minute.
Oribe Peralta set up the goal with an excellent pass that put Hernandez in space and he took a touch before thrashing a fierce effort beyond Honduras goalkeeper Donis Escober.
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.
Marco Fabian swung in a corner from the left and unmarked Oswaldo Alanis nodded into the top-right corner from nine yards in the 37th minute.
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.
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