Also on Friday, Jim Fleming was relieved of his duties as special assistant to the president of baseball operations.
"The Marlins organization has decided to make some changes at the helm of our baseball operations," team owner Jeffrey Loria said in a statement. "Effective immediately, I have relieved Larry Beinfest of his duties so that he may pursue other opportunities.
"Larry has worked with me for 13 years, making huge contributions to our efforts and serving as a partner to me in the process. I wish him nothing but the best and know he will make a great addition wherever he lands."
Beinfest was at the helm when the Marlins won the 2003 World Series. Under his watch, the club had winning seasons from 2003-05, as well as in 2008-09. But the team has gone through four straight losing seasons.
For more than a week, there had been speculation that Beinfest's position was in jeopardy.
"I want to thank the Marlins for the opportunity. I look back positively at tackling numerous challenges, opening a new ballpark and enjoying a World Series Championship," Beinfest said in a statement sent to the Miami Herald and Sun-Sentinel. "I worked with some tremendous players and staff in Miami and appreciate their friendship and professional respect. I look forward to continuing my career in the near future."
Under contract through 2015, Beinfest was rumored to be departing last September, but he remained for one more year.
At this point, the Marlins haven't announced who will take over as president of baseball operations. But there is growing speculation that Dan Jennings, vice president of player personnel and assistant general manager, will get the position.
"I will soon be making further announcements in terms of our new structure in baseball operations," Loria said in a statement.
The announcement was made by the organization about the time the Marlins were taking batting practice in preparation for their season-ending series against the Tigers at Marlins Park.
The team didn't conduct a formal news conference regarding the decisions.
During his media session, manager Mike Redmond spoke briefly about the front-office shakeup.
"Being around the game as long as I have, I've been through this scenario before, where change happens, whether it is a manager or a general manager," Redmond said. "Change happens. It's part of the game. You obviously don't like to see it, but at the same time, it's part of the game. You've got to be able to go forward."
Throughout his tenure, Beinfest gained praise for making shrewd deals, often moving higher-priced players for upstart prospects.
The first of many major trades under Beinfest's watch came on March 27, 2002. The Marlins sent Antonio Alfonseca and Matt Clement to the Cubs for a package that included lefty Dontrelle Willis, who went on to be the National League Rookie of the Year in 2003.
Willis was the first major impact acquisition.
The Marlins also made a blockbuster trade with the Tigers in 2007, sending Miguel Cabrera and Willis to Detroit for six prospects, headlined by Cameron Maybin and Andrew Miller. That move didn't pan out for Miami.
More recently, the Marlins have reshaped their roster twice since moving into Marlins Park in 2012.
The organization made a big splash, going "all-in" prior to '12, and boosted payroll to a record $100 million. It signed high-profile free agents Jose Reyes, Mark Buehrle and Heath Bell. The Marlins also brought in Ozzie Guillen as manager.
But the team didn't click, and by midseason, the Marlins made four major trades prior to the July 31 non-waiver Trade Deadline. They sent Hanley Ramirez and Randy Choate to the Dodgers for Nathan Eovaldi. Omar Infante and Anibal Sanchez were sent to the Tigers for Jacob Turner, Rob Brantly and Brian Flynn.
They also dealt Edward Mujica to the Cardinals for Zack Cox, and Gaby Sanchez was sent to the Pirates for Gorkys Hernandez and a compensatory pick in the 2013 First-Year Player Draft.
After a disappointing 69-93 season in '12, the Marlins completed a 12-player blockbuster deal with Toronto last November. They shipped Reyes, Buehrle, Josh Johnson, Emilio Bonifacio and John Buck to the Blue Jays for seven players, highlighted by Adeiny Hechavarria, Henderson Alvarez, Jeff Mathis and Jake Marisnick.
Miami's payroll was roughly $37 million this season, and the club enters the final weekend at 59-100.