The Baseball Hall of Fame said MacPhail died Thursday in Delray Beach, Fla.
MacPhail was general manager for the Baltimore Orioles and New York Yankees, then served as AL president from 1973-83. He was elected to the Hall of Fame in 1998 by the Veterans Committee.
"Lee MacPhail was one of the great executives in baseball history and a Hall of Famer in every sense, both personally and professionally," said baseball commissioner Bud Selig in a statement Friday. "I had great admiration for Lee as American League president, and he was respected and liked by everyone with whom he came in contact. His hallmarks were dignity, common sense and humility. He was not only a remarkable league executive, but was a true baseball man as is evidenced by his brilliant leadership of the storied New York Yankees and Baltimore Orioles franchises. Lee always put the interests of the sport first and through his love of the game taught all of us to cherish it in every way. Major League Baseball and all of our clubs feel a great sense of loss today, and I send my deepest condolences to one of the first families of the national pastime."
MacPhail's start in baseball came with the Brooklyn Dodgers and he soon moved to the New York Yankees as farm director in the late 1940s. The Yankees won seven World Series titles from 1949-58 before MacPhail left to take over as general manager of the Orioles.
After leaving Baltimore in 1965, MacPhail went back to the Yankees as GM in 1966. He left after the 1973 season, spending only one year as the first general manager under George Steinbrenner's ownership, then was soon selected as AL president in October 1973. He retired as league president after the 1983 season.
MacPhail was the son of Hall of Fame executive Larry MacPhail and the father of Andy MacPhail, who served front office roles with the Twins, Cubs and Orioles.