Minaya, 53, became the first Hispanic general manager in baseball history when the Montreal Expos hired him in 2002. He ran the Mets from 2004 through 2010, when he was fired along with manager Jerry Manuel.
Minaya will work for new Padres general manager Josh Byrnes and will remain based in New Jersey, his longtime home.
"I did enjoy the quality time I felt with my family," Minaya said of his year away from the game. "One thing I missed was the competition."
After signing Pedro Martinez and Carlos Beltran, the Mets came within one win of the 2006 World Series. But New York faded in September in both 2007 and 2008, then was decimated by injuries in 2009 and 2010. The Mets fired Minaya after the 2010 season.
"His experience, knowledge, evaluative skills and connections throughout the industry will be invaluable for us," Byrnes said.
Minaya's salary will be offset from the approximately $1.4 million the Mets owe him next year in the final season of his contract.
Minaya recently interviewed for the Los Angeles Angels GM position, but lost out to Jerry Dipoto. Toronto, Cleveland and Boston are among other clubs that had considered hiring him in a scouting or advisory capacity.
ESPN.com senior baseball writer Jerry Crasnick and The Associated Press contributed to this report.