Terms were not disclosed, but according to multiple reports, Green received a three-year extension, putting him under contract with the Padres through the 2021 season.
"Throughout the past two seasons, Andy has consistently proven to us his leadership abilities and strong character," vice president/general manager A.J. Preller said in a statement. "Andy's knowledge of the game and passion for his players has earned him respect in the clubhouse and throughout the organization. As we continue to build a system that produces winning baseball from top to bottom, I am confident that Andy provides the leadership and stability needed to deliver a championship to San Diego."
Green, 40, said in the statement that he was "both excited and motivated by the opportunity to continue to lead our players as we build a championship-caliber club for the fans of San Diego."
He is 119-159 as the Padres' manager, including 51-65 this season.
"We remain committed to our plan to build a championship team with homegrown talent, and we are confident in the direction we are moving as an organization," Padres executive chairman Ron Fowler and managing partner Peter Seidler said in the statement. "Andy is invested in the development of our players at all levels, both as athletes and as people. His managerial style is characterized by intelligence, preparation and integrity, and he has continually proven himself to be the right person to lead this young team. We look forward to him managing, motivating and teaching the many waves of talent that we know are on their way to San Diego."