MacPhail died Thursday in Delray Beach, Fla., the Hall of Fame said. An announcement on the hall's website said MacPhail died "peacefully Thursday evening of natural causes at his home."
He served as general manager of the Baltimore Orioles and New York Yankees before working as American League President from 1973-83. While he was president, the American League added franchises in Toronto and Seattle.
MacPhail was seen as having a key role in ending in the 1981 baseball strike.
He was involved in professional baseball for 45 years.
"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.
"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 MacPhail's father, Larry MacPhail was also a baseball executive who was elected to the Baseball Hall of Fame. They are the only father-and-son duo to be inducted into the hall.