Dipoto, who was given the title of executive vice president and general manager of baseball operations, will be formally introduced at a news conference Tuesday in Seattle.
Dipoto, 47, had been at the forefront of the Mariners' search since Zduriencik was dismissed on Aug. 28. Dipoto not only has experience as a GM, he worked in the American League West the past 3 1/2 seasons before resigning from the Angels on July 1 after reported conflicts with long-time manager Mike Scioscia.
"Jerry impressed us at each step of the process," Mather said. "He has a very unique skill set, having been a successful player in the Majors, then moving into front offices with steadily increasing responsibilities. Jerry has scouted, spent time in player development and has a track record as a very successful general manager."
Dipoto is a former Major League pitcher who is considered to be strong in analytics and scouting. The Angels went 89-73 his first year in 2012, 78-84 in 2013 and 98-64 last year. They're currently 81-74 and a half-game back of the Astros in the race for the AL's final Wild Card spot, with former GM Bill Stoneman running the club since Dipoto's departure.
Mather said Dipoto's familiarity with the Mariners was a big plus.
"During our conversations over the past few weeks, it became clear to me that he has a very solid understanding of our team and organization, both where we are and where we want to be," Mather said. "And he has a strategy to get us there. Few candidates bring the combination of playing the game, scouting, a solid understanding of statistical metrics and a plan for player development. I am looking forward to having Jerry lead our baseball operations for a long time."
During his time with the Angels, Dipoto's biggest moves included the signing of free agents Albert Pujols, Josh Hamilton, C.J. Wilson and Joe Smith, and making trades for Huston Street, Zack Greinke, David Freese, Chris Iannetta, Hector Santiago, Tyler Skaggs and Andrew Heaney.
After resigning from the Angels, Dipoto told MLB.com that he regretted leaving in midseason, but believed "it was the right thing to do for my own position, my own state of mind, my family. ... I felt like I was in a position where I wasn't able to help the club get better in the way that I wanted to."
Dipoto had been working as a special consultant with the Red Sox since August. He initially worked for the Red Sox as a scout in 2003, then went on to become scouting director for the Rockies and D-backs.
Dipoto worked as interim GM for the D-backs after Josh Byrnes was let go in midseason in 2010, then was hired by the Angels to be their GM in 2011.
Mather had been interviewing candidates for the past month, with Yankees assistant GM Billy Eppler also among those receiving a second interview.
Mariners assistant GM Jeff Kingston has been running the team since Zduriencik's departure.
Dipoto becomes the ninth GM in Mariners history, joining Lou Gorman (1977-80), Dan O'Brien (1981-83), Hal Keller (1984-85), Dick Balderson (1986-88), Woody Woodward (1989-99), Pat Gillick (2000-03), Bill Bavasi (2004-08) and Zduriencik (2009-15).