Black has a 464-509 record in six seasons managing the Padres, with winning records in 2007 and 2010.
Black, who was already under contract through 2013, was named the National League's Manager of the Year by the Baseball Writers' Association of America in 2010.
"Buddy has a keen insight into team dynamics and creates a great environment for the players and coaching staff," Padres general manager Josh Byrnes said in a statement.
"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."
In 2012, the Padres finished 76-86 with a fourth-place finish in the NL West after a slow start that was caused in part by underperformance and a slew of early-season injuries.
The Padres went 49-37 over their final 86 games, posting a .570 winning percentage that ranked as the fifth-best among all NL teams from June 28 to the end of the regular season.
Black, hired before the 2007 season, was given a three-year contract extension in July 2010 with club options for 2014 and 2015.
The 2010 season saw the Padres win 90 games, finish second in the NL West and miss the postseason by one victory after losing on the final day of the regular season to the Giants, who went on to win the World Series.
"I think the biggest thing for me," Padres second baseman David Eckstein said in 2010, "is that he never shows any panic."
Black is working under his third general manager in Byrnes. He was hired by Kevin Towers -- now the GM in Arizona -- before the 2007 season and received his extension in 2010 while Jed Hoyer -- the current GM of the Cubs -- presided over the team.
"I am honored and humbled by the faith Josh and our ownership team have shown in me, the coaching staff and our players," Black said in a statement.
"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's six seasons as manager of the Padres rank only behind Bruce Bochy, who managed the team for 12 seasons from 1995-2006.