The Pontiff, who flew in from Mexico, was welcomed to the eastern city of Santiago by President Raul Castro.
Pope Benedict XVI said he had come as a pilgrim of charity, and would pray for peace, liberty and reconciliation.
The Pope also expressed sympathy for the “just aspirations” of all Cuban people, wherever they were.
Pope Benedict then celebrated Mass before an estimated crowd of some 200,000 in Santiago’s Revolution Square.
He appealed to the audience to reinvigorate their faith “that you may strive to build a renewed and open society, a better society, one more worthy of humanity”.
Before the mass, one man was arrested after shouting: “Down with communism”. Others in the audience booed him for spoiling the atmosphere and shouted “Cuba, Cuba, Cuba”.
President Raul Castro was among those attending the service.
In his speech at the airport, President Raul Castro said socialist Cuba allowed full freedom of religion and enjoyed good relations with the Catholic Church.
Raul Castro said Cuba shared the Pope’s concerns over global poverty, inequality and environmental destruction.
And he stressed that Cuba was determined to defend its independence in the face of the US embargo.
Both leaders looked back to the visit by the late Pope John Paul II 14 years ago, which Pope Benedict said “was like a gentle breeze that gave new strength to the Church in Cuba”.
Ahead of his visit, Pope Benedict had suggested Cuba’s Marxist structure “no longer corresponds to reality” and called for the adoption of a “new model”.
But on his arrival, he recognized Cuba’s efforts to “renew and broaden its horizons”.
Observers say relations between Church and state have warmed in Cuba in recent years.
Raul Castro has accepted the Church’s mediation on issues such as political prisoners, recognizing its position as the most influential organization outside the communist government.
The Pope’s visit is seen as an effort to further improve relations and increase the role of the Church in Cuban society at a time of rapid change.
Pope Benedict’s visit to Santiago coincides with the 400th anniversary of the discovery of the icon that is Cuba’s patron saint, the Virgin of Charity of El Cobre, which he cited as the main reason for his trip to the island.
Found floating in a bay in 1612 by fishermen, the icon was revered by Cuba’s independence heroes and sits in the foothills of the Sierra Maestra mountains from which Fidel Castro and Ernesto “Che” Guevara staged the 1959 Cuban revolution.
The Pope is expected to make a private visit to the sanctuary where the icon is housed before travelling to Havana later this week for private talks with President Castro.
Church officials have said there is no time in his schedule to meet dissidents.
Opposition groups say dozens of dissidents were detained ahead of the visit, and others were prevented from attending the service in Santiago.
Pope Benedict’s trip to Cuba follows a visit to Mexico, where he celebrated a huge open-air Mass at the Christ the King monument in the central city of Silao.
He urged the 500,000 Catholics gathered for the sermon to look to their faith in response to poverty and crime and to reject violence and revenge.
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