The Mozambican-born Eusebio died of cardio-pulmonary arrest at 0430 GMT, the club said.
Eusebio, the 1965 European Footballer of the Year, is considered one of the best footballers of all time and best ever from Portugal.
During his career with Benfica the Lisbon side won the European Cup in 1962. He scored 733 times in 745 professional matches.
Nicknamed the 'Black Panther', he also helped Portugal take third place in the 1966 World Cup, where he was top scorer with nine goals.