Hernandez, who turns 24 on June 1, had initially been called up for the Olympic tournament as one of Mexico's three over-age players and had even been suggested as a possible flag-bearer at the opening ceremony.
However, United have agreed with the Mexican FA he will have the full summer off instead.
United boss Sir Alex Ferguson told the club's website: "His form last season was fantastic.
"He's found the second year more difficult, but a lot of that is down to not having a summer break for three years and playing every summer for his country.
"Next year he will be fine as we have agreed with the Mexican Football Association that he is going to get the requisite rest he needs to perform in the Premier League."