No other Padres employee will be leaving the organization, according to a source, and San Diego will receive a player to be named later as compensation for losing Hoyer.
Earlier in the week, Hoyer -- who just completed his second season as the Padres' GM and still had two seasons remaining on his contract -- was linked to Epstein and the Cubs as was McLeod, who, like Hoyer, previously worked with Epstein in Boston.
The Padres are expected to promote Josh Byrnes, vice president of baseball operations, to general manager.
Byrnes was the GM of the D-backs from 2005-10, hired by current San Diego vice chairman and CEO Jeff Moorad and was later awarded an eight-year extension following the 2007 season, when the D-backs advanced to the National League Championship Series.
The Padres hired Byrnes in December, and he assisted Hoyer in several areas. He also helped scout in preparation for the First-Year Player Draft in June.
McLeod, who has run the past two Drafts for the club, did the same in Boston before joining the Padres in December 2009.
Hoyer and Epstein worked together from 2002 up to the point when Hoyer was hired by Moorad to be the Padres' GM in October 2009. Byrnes worked as Epstein's assistant before becoming GM of the D-backs.
As for Epstein, he officially resigned on Friday, a long-anticipated move that took time as the two teams determined -- or attempted to determine -- compensation.
In the joint statement released by the Red Sox and Cubs on Friday, the two sides have agreed upon "a process by which appropriate compensation will be determined for the Red Sox and that issue will be resolved in the near term."