After the position went to Padres manager Bruce Bochy, Black became a candidate for the Padres job, and was officially hired on November 8, 2006. Despite a last place finish for the Padres in 2008, Black returned to finish his contract in 2009. During the 2009 season, Black was given a contract extension for the 2010 season with a club option for 2011. During the 2010 season, the Padres gave Black another three-year extension through 2013, with club options in 2014 and 2015. In 2010, Black presided over the worst collapse in Padres history when they went on a ten-game losing streak with a little over a month left in the season, went 12-16 in September and squandered a 6 1/2 game lead over the Giants for the NL West title. Black nonetheless was the winner of the 2010 National League Manager of the Year Award, edging Dusty Baker of the Cincinnati Reds in voting by a single point. Black is only the third former full-time pitcher to win a Manager of the Year Award, joining Tommy Lasorda and Larry Dierker.
On June 15, 2015, Black was fired after eight-plus seasons with the Padres after the team started 2015 at 32–33 and was six games behind in the National League West.
Black was born to Canadian parents in Northern California. He has a wife, Nanette and two daughters. His wife is a pediatric ICU nurse. His older daughter attended Oregon State University and is currently an interior designer while his younger, a collegiate gymnast, graduated from the University of Maryland with a degree in math and kinesiology in 2014.