It was not the first time Vela has decided not to play for his country, having declined in May to be a part of Mexico's Olympic squad that won the London gold medal because he would be in pre-season training with his club Real Sociedad.
Vela, who also turned down Mexico for the 2011 CONCACAF Gold Cup, was suspended by Femexfut for six months in 2010 for his part in an unauthorised party at the team hotel after a friendly.
"On Tuesday, I spoke with coach (Jose Manuel) De la Torre, a very open conversation. I was the one who asked not to be picked for strictly personal reasons," the 23-year-old former Arsenal forward said.
"I wanted him to know and he respected my decision. I'll talk about the personal issues in the future and at I time when I think it appropriate," he told a news conference in a video posted on his club's website.
Mexico host Jamaica at the Azteca in Mexico City on February 6 in their opening match of the final six-nation group in the CONCACAF region's qualifiers.
Costa Rica, Honduras, Panama and the United States are also in the group from which the top three will qualify for the 2014 finals in Brazil. The fourth-placed team will play off against the Oceania winners for another ticket to the finals.
"You can't condition the national team. I don't want anyone who isn't happy, I don't need to bring in a player who's going to be uncomfortable," said De la Torre.
"I'll never close the door to anyone but I do have to watch how (the players) behave in all aspects," he told Mexico's Estadio W radio.
Striker Javier Hernandez of Manchester United, winger Andres Guardado of Valencia, Espanyol defender Hector Moreno and Mallorca forward Giovani dos Santos are the European-based players chosen by De la Torre, Femexfut said.
Ajaccio goalkeeper Guillermo Ochoa has not been included as his son is due in the coming days.