PSV midfielder Andres Guardado and Porto fullback Miguel Layun are the other prominent picks, but coach Juan Carlos Osorio left former Arsenal striker Carlos Vela out of the lineup.
Hernandez played at Manchester United and Real Madrid before joining Bayer for the 2015-2016 season, finishing fourth best scorer with 17 goals.
There are a total of nine Europe-based players.
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Veteran defender Rafael Marquez, 37, who was once a stalwart at Barcelona and now plays for Mexican club Atlas, was brought in because "he is very much needed on and off the pitch," Osorio said.
"It's a team with several mixed and multi-purpose players," Osorio, who is Colombian, said at a news conference.
But Vela, who plays for Spain's Real Sociedad, and former Barcelona player Giovani dos Santos, who now plays of Los Angeles Galaxy, were the biggest omissions.
"Carlos is not going through his best moment and his absence was discussed with him," Osorio said.
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Vela only scored five goals this year, his worst return in four seasons at Real Sociedad. He was also sidelined by his club coach, Eusebio Sacristan, in March for missing practice after going to a concert in Madrid.
Osorio said dos Santos had "declined the invitation" to join the team, but the coach declined to elaborate.
Mexico was drawn in Group C at the Copa to be played in the United States. They open against Uruguay on June 5, followed by Jamaica on June 9 and Venezuela on June 13.
Squad:
Goalkeepers: Alfredo Talavera (Toluca/MEX), Jesus Corona (Cruz Azul/MEX), Guillermo Ochoa (Malaga/ESP).
Defenders: Paul Aguilar (America/MEX), Nestor Araujo (Santos/MEX), Diego Reyes (Real Sociedad/ESP), Hector Moreno (PSV/HOL), Yasser Corona (Queretaro/MEX), Jorge Torres (Tigres/MEX), Miguel Layun (Porto/POR), Rafael Márquez (Atlas/MEX).
Midfielders: Jesus Molina (Santos/MEX), Hector Herrera (Porto/POR), Jesus Duenas (Tigres/MEX), Andres Guardado (PSV/HOL), Carlos Pena (Guadalajara/MEX).
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