Plantier, 42, replaces Randy Ready, who was dismissed the day after the conclusion of the 2011 season. Only the Giants scored fewer runs than the Padres in the National League.
The hiring was initially reported by FOX Sports' Ken Rosenthal.
The person who hired Plantier, Josh Byrnes, will be officially introduced as executive vice president/general manager at a press conference Monday.
Plantier just completed his first year in the Padres organization. He began the season as the hitting coach for Class A Lake Elsinore before taking over as manager midway through the year.
An 11-round pick in the 1987 First-Year Player Draft by the Red Sox, Plantier finished eighth in the American League Rookie of the Year voting in 1991 when he compiled a 1.034 OPS (on-base plus slugging) mark for the Red Sox in 174 plate appearances.
After a 1992 season in which he slumped to a .246 average, the Red Sox dealt him to the Padres.
Plantier responded by slugging 34 homers and driving in 100 runs for the Padres.
It was the first of three stints that Plantier would spend with the Padres, who sent him to the Astros after the 1994 season in an 11-player trade that brought Ken Caminiti and Steve Finley to San Diego.
Plantier did not stay away long as the Astros traded him back to the Padres midway through the 1995 season and after spending 1996 with Oakland, he returned to the Padres in 1997.
In parts of eight big league seasons, Plantier finished with a career OPS of .770.
After retiring from baseball, Plantier earned a bachelor's degree in social science from California State University San Marcos.
Plantier began his coaching career in 2008 as hitting coach for Seattle's Double-A West Tennessee affiliate and he managed that team in 2009 before being named Minor League hitting coordinator for the Mariners in 2010.