Hernandez had initially been called up for the Olympics, but United manager Alex Ferguson says the club has agreed with the Mexican Football Association that the striker is "going to get the requisite rest that he needs to perform in the Premier League."
Hernandez will play in Mexico's two qualifiers for the 2014 World Cup at the start of June.
Then he will have a full summer's rest for the first time in three years before the start of his third season at United in August.
Mexico's opening match at the Olympics is July 26 against South Korea.
(For more sports news and updates, follow Ahram Online Sports on Twitter: @AO Sports)