The 84-year-old pontiff met with the Castro brothers separately and had talks with Fidel Castro, 85, at the Vatican Embassy in Havana. Younger brother Raul Castro took over as Cuba's leader from Fidel.
The Vatican's excommunication of Fidel Castro in 1962 is predated only by the U.S. sanctions on Cuba, the oldest in history, and followed Castro's expulsion of nuns and priests and confiscation of church property.
Cuba relaxed Christmas celebrations, banned in 1969, in preparations for Pope Benedict's visit but the Vatican gave no indication that Fidel Castro could return to the Catholic Church.
In a meeting peppered with pleasantries, Castro asked what a pope did, Cuban media reported, to which Benedict replied with details of his routine.
Cuban opposition groups welcomed the pope's visit but expressed regret he didn't meet their activists or give them an opportunity to air grievances. The opposition said the pope's meeting with Fidel Castro, who no longer officially holds an office, would be seen as a legitimization of the communist state.
The Vatican is apparently hoping its strategies can steer Cuba toward God and religion. During a public mass, Benedict commented on the absence of God from Cuban society and called for more tolerance of religious practice and public acceptance of the Catholic Church.
The pope began his first visit to Spanish-speaking Latin America last week with a stop in Mexico. He arrived in Cuba in time for the 400th anniversary of Cuba's Catholic patron, Our Lady of Charity of El Cobre.
Unlike Pope John Paul II, who visited every Latin American country before his death in 2005, Benedict is just starting to engage with his Catholic audience in the region. He visited Portuguese-speaking Brazil in 2007.
On his flight to Mexico, the pope said that Marxism was discredited and Cuba was in need of a new model to replace the receding communist system.
Cubans are constantly reminded of how to transport themselves from the loosening bonds of communism into the embrace of an as yet undefined socialist capitalism of the Chinese variety.
The numbers of practicing Christians have dwindled in Cuba but church leaders hope political liberalization may draw the people back to religion. Only about 1-10th of the 11 million Cubans admit to being religious but church leaders say that will change for the better.
On the flip side, Latin America's Catholic leaders want more representation in the Vatican and more voting rights for Latin American cardinals in the councils of the Vatican.
A European majority in the electing cardinals' body in the Vatican means whoever succeeds German-born Benedict may also be European rather than Latin, church leaders say.