General Manager Josh Byrnes said Black, who has compiled a 464-509 record in six at the helm, has the Padres headed in the right direction after they went 49-37 over the final 86 games of the year.
"Buddy has a keen insight into team dynamics and creates a great environment for the players and coaching staff," Byrnes said. "He is a gifted leader with a terrific mind for the game and a genuine interest and curiosity related to all areas of our organization."
The 2010 National League Manager of the Year has not been able to take the Padres into the post-season during his tenure, however, guiding them to an overall 76-86 record in 2012.
"I am extremely proud to be part of this organization, and I'm excited to continue working with ownership and our baseball operations team toward achieving our ultimate goal: bringing a championship to the great city and fans of San Diego," Black said.