Financial terms and length of contract were not disclosed.
Last season, the Diamondbacks finished 81-81 for the second straight year.
In 2011, Gibson led the team to a 94-68 record and an National League West division title, earning him the NL Manager of the Year award. They lost in the National League Division Series to the Milwaukee Brewers three games to two later that season.
JAFFE: Winter Report Card: Arizona Diamondbacks In four seasons with the team, Gibson has complied a 290-278 record.