Moorad, though reluctant to lose Hoyer, the source said, said he would not grant him the extension and told him he was free to take the Cubs' job.
In another Cubs staffing development, has confirmed that Padres assistant GM Jason Mc Leod will also join Epstein and Hoyer in Chicago.
One of Epstein's first chores in Chicago is the future of manager Mike Quade, who led the team to a 71-91 record in his first full season. Under Epstein's guidance, Boston went 839-619 (.575) in the regular season and 34-23 in the playoffs, winning more than 90 games in all but two seasons.
Byrnes was GM of the Arizona Diamondbacks when Padres owner Jeff Moorad was part-owner of that team.
Major League Baseball generally prohibits announcements during the World Series, but Friday is a day off between Games 2 and 3 between the Cardinals and Rangers.
A source told ESPNBoston.com's Gordon Edes that Red Sox assistant GM Ben Cherington will be named Epstein's successor.
He was 12-12 with a 6.41 ERA in 28 starts for the Red Sox in 2011.
But the expected agreement will include Cubs minor leaguers, although not top prospects Brett Jackson, Trey Mc Nutt or Matt Szczur, the source said. What is clear is that Jed Hoyer will be Epstein's general manager in Chicago.