According to the Padres, a California-based ownership group led by Jeff Moorad will buy the team over time - up to five years - and eventually become the full owners.
Padres officials declined to divulge the sale price, but the deal is reported to be worth more than $400 million.
Under the terms of the agreement, the sale is expected to close and Moorad become the Padres' chief executive officer by opening day, according to a statement from the franchise.
Moorad, a former player representative for professional baseball and football players, resigned last month as chief executive officer of the Diamondbacks. He purchased an ownership state in the Diamondbacks in 2005.
"It's a honor to enter into an agreement to purchase the San Diego Padres, a team with a rich history of great players, terrific fans and a strong commitment to the community,'' Moorad said. "I consider it a privilege to have worked out an agreement that allows for the orderly transition of ownership of the franchise over the next several years.''
John Moores bought the Padres in 1995 for about $80 million. In December, Moores announced the hiring of Goldman Sachs to look for potential buyers.
"Jeff Moorad will not only bring to the Padres his unique experience, passion for the game and proven leadership, but an unparalleled commitment to the city of San Diego and its dedicated fans,'' Moores said. "I speak for our entire organization in saying that we look forward to working with Jeff to reach the ultimate goal of winning a World Series title for America's Finest City.''