The Padres have exercised their contract options on Black for the 2014 and 2015 seasons.
"Buddy has a keen insight into team dynamics and creates a great environment for the players and coaching staff," said [general manager Josh] Byrnes.
"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."
Black has been at the helm in San Diego since 2007, leading the Padres to a .477 record (464-509) in his six years in charge. The former Angels pitching coach led the Padres to a 90-72 mark in 2010, giving San Diego just their fourth 90-win team in franchise history and earning Black the National League Manager of the Year award.
The Padres finished the 2012 season at a disappointing 76-86 mark, but put together a strong second half, going 49-37 over the team’s final 86 games.