Haeger was 10-13 with a 4.45 ERA in 28 games (25 starts) for Triple-A Charlotte, the top Minor League affiliate for the White Sox. He was designated for assignment by the White Sox on Sept. 6.
"I've always felt a knuckleballer could potentially be successful here, pitching on the coast with the dense air," Padres general manager Kevin Towers said. "We're hoping he's a late-bloomer."
Haeger, the White Sox first-round pick (25th overall) in 1999, made his Major League debut in 2006. In parts of two Major League seasons, Haeger is 1-2 with a save and a 4.85 ERA.
Haeger has honed his knuckleball craft with Charlie Hough during Spring Training and later talked with Boston's Tim Wakefield about the pitch.
He is expected to join the Padres on Friday.
Corey Brock is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.