The Philadelphia Phillies have dismissed
"It's never an easy decision to make a change," MacPhail said in a statement. "Ruben has had a direct impact on some of the best years in the team's history. He helped to create some great memories for Phillies fans with his accomplishments, but in order to return to a top-contending club, we believe this is the right thing to do as we continue the rebuilding process."
Assistant general manager Scott Proefrock has been given the interim title while the team begins a search for a replacement.
The Phillies (54-86) have the worst record in the majors at 54-86 and will miss the postseason for the fourth straight year after winning five consecutive NL East titles. Amaro replaced Pat Gillick, who retired after the Phillies won the 2008 World Series and took over as team president last year. Amaro previously served 10 years as assistant GM.
Amaro has engineered several trades during Philadelphia's rebuilding process, including dealing ace Cole Hamels to Texas and 2007 NL MVP Jimmy Rollins and six-time All-Star Chase Utley to the Dodgers.
Amaro, 50, rose from team batboy in 1980-83 to playing for the Phillies for five seasons in the 1990s. He guided the Phillies to the 2009 National League pennant and division titles and three division titles.
"The Phillies ownership fully supports Andy's decision not to extend Ruben Amaro's contract," co-owner John Middleton said in a statement. "As a group, we have tremendous respect for Ruben, who has been a significant contributor to this organization. This decision is about taking the club in a new direction, and that will be facilitated by new leadership."
Manager Ryne Sandberg resigned in June. MacPhail was hired a week later to replace Gillick as president after the season.
The Associated Press contributed to this report.