Throughout his visit the Pope has made thinly-veiled references to Cuban dissidents, and the need for economic reforms.
On his departure his last message was aimed at the United States.
"Cuba could build a society of broad vison, renewed and reconciled," he said, but it was more difficult "when restrictive economic measures, imposed from outside the country, unfairly burden its people."
Earlier Benedict had welcomed Fidel Castro at the Vatican embassy in Havana. The 85-year-old is the brother of president Raul Castro and the island's first revolutionary leader. During the half-hour meeting, Castro asked the Pontiff to choose a book for him to read and to reflect upon.