The Red Sox made an official announcement Monday.
"I am truly honored to join the Red Sox," Amaro said. "I am poised, focused and ready to bring anything I can in terms of experience and knowledge to this position, and I look forward to being a part of the Boston Red Sox."
Amaro, 50, took over as the Phillies' GM shortly after the team won the 2008 World Series and held the role until September, when incoming president of baseball operations Andy MacPhail announced the club would not be renewing his contract. The Phillies have hired Los Angeles Angels assistant GM Matt Klentak as Amaro's replacement.
Amaro, the son of former big leaguer Ruben Amaro Sr., spent eight years in the major leagues as an outfielder with the Angels, Phillies and Indians. He was a .235 career hitter in 485 games with those three clubs from 1991-98.
The Miami Marlins bucked tradition in May when they fired manager Mike Redmond and moved general manager Dan Jennings to the dugout to replace him. Jennings guided the Marlins to a 55-69 record and has since returned to his role in the front office, while the Marlins are conducting a search for a new manager.
Amaro replaces former Red Sox first-base coach Arnie Beyeler, who was not retained for the 2016 season.