During the service, the red-white-and-blue Cuban flag stands directly behind Cardinal Jaime Ortega as he implores followers not to look to the skies for God but to see the Almighty in the faces of "subversives," the poor and prisoners.
Outside the old stone cathedral, beggars sit upright on the ground four abreast on either side of the exit, holding their hands heavenward in gestures of supplication to the hundreds of worshippers as they leave at the end of Mass.
This is the face of the church in Cuba, a slowly growing institution that is looked upon for food, medicine, and spiritual hope in a society that has struggled through nearly a decade of economic depression since the breakup of the Soviet Union and the loss of the $6 billion a year subsidy Moscow once provided.
In 1998, when Pope John Paul II came to visit and hundreds of thousands poured into fields in Santiago and the Plaza of the Revolution in downtown Havana for public Masses, there was hope in some circles that Cuba would follow Poland's example and the walls of political oppression would come tumbling down amid public expressions of religious freedom.
That scenario was unrealistic, Cuban observers now admit. The church has fought hard to maintain itself as the only significant independent organization in this island nation of 11 million. However, the Catholic Church's careful expansion of its influence in areas from education to humanitarian aid occurs on the razor's edge of independence, where there is a recurring fear that one day it will be cast back into the 1960s and 1970s, when believers were harassed or imprisoned.
The Cuban government allowed four days of freedom when Pope John Paul II came to the island, said Havana Bishop Alfredo Petit.
"After that, the teacher said, `Boys, the playtime is over,'" Petit said.
The case of Elian Gonzalez once again focused attention on Cuba and the role of the Catholic Church. With only an estimated 2,500 political dissidents on the island, the church is seen as the only institution outside the government capable of generating social change.
An estimated 40% of the people in the country are baptized Catholics, but the percentage of those connected to the church rises to 60% when one considers all the services people seek at significant moments in their lives, from births to funerals.
But parallels to Poland in the 1980s end there. When it gets right down to who comes to church in Cuba, after 40 years of often-bitter persecution, less than 2% are considered active Catholics, according to church officials.
"The people, they are afraid," said Archbishop Luis Robles Diaz, papal nuncio to Cuba.
With good historical reason. In 1961, shortly after the revolution, Fidel Castro, once an altar boy, expelled 130 priests. Some others, like now-Cardinal Ortega, were tossed into prison camps.
The climate for religious freedom, however, has improved dramatically since 1992, when Cuba officially became a secular rather than an atheist state, and Communist Party members were permitted to belong to churches. In the months before the papal visit, the Cuban government allowed more foreign priests to enter the country and gave permission for outdoor processions and other public displays of religion.
Starting in 1997, in a huge morale boost for the Christian community, the country was once again allowed to celebrate Christmas publicly.
With the freedom, some of the fear has dissipated.
Fifty-one-year-old Ofelia Matos, a sewer operator and party member, returned to the Catholic faith of her parents after the 1992 law made it possible.
"People don't have to be afraid as they were before to come to church," said Matos, wearing a wooden cross over a white blouse outside the cathedral. "With God, nothing is impossible. I search for the truth inside the Catholic Church. I realize the truth lies in the spirit of God."
The church is still not allowed to open parochial schools and is severely restricted in its ability to publish materials and speak on radio or television. There are limits on visas for foreign priests and building permits for new churches, and newfound freedoms of outdoor worship and door-to-door evangelization rest on tentative ground.
What it has on its side is a traditional place in Cuban culture and the diplomatic authority of the Vatican in shaping international opinion.
"The breathing room doesn't come easy. The church's strength is its persistence and its appeal. Time is on their side," said Thomas Garofalo, director of the Cuba Program for the U.S.-based Catholic Relief Services. "They continue to be the only institution in Cuban society that can convoke the people except the government."
Slowly, that role is expanding, particularly in the area of social services, where the church is filling in some of the growing cracks in Cuba's struggling economy. Government wariness of the people depending on any independent institution for aid is giving way to practical concerns for unmet basic needs and pressure from below to accept relief.
At a nursing home run by sisters in Havana, people with pull try to get their relatives into the clean, friendly facility that is a step up from state-run homes.
At St. John Lateran Church, where block-by-block evangelism grids of the surrounding neighborhood are posted inside the church and attendance at Sunday masses has grown from 150 in 1996 to 550 today, classes in subjects from catechism to computers to Cuban culture are offered in a series of underground rooms.
"We're not going against anybody. We're going in favor of Jesus of Nazareth and the Cuban person, with a lot of prudence," said the Rev. Manuel Una.
One thing 40 years of harassment has provided is a remnant of believers who are fiercely committed to an independent church, observers said.
In Pinar del Rio, Dagoberto Valdes, a Catholic intellectual, publishes the independent magazine Vitral under the auspices of the diocese.
In a meeting with lay volunteers at a parish in Matanzas, they talk about finding ways to do ministry such as claiming to be relatives of prisoners to get inside jails to visit people abandoned by Cuban society.
The Rev. Donald Cozzens, rector of St. Mary Seminary in Wickliffe, Ohio, and a member of a small U.S. Catholic Relief Services delegation to Cuba in early June, said he returned with a deep respect for the institutional church and the "remarkable" faith of practicing Catholics in Cuba.
"When your backs are against the wall, when at least theoretically there is the possibility of having the seminary or churches closed, you...fall back on the Gospel," he said. "You have to ask what really matters."
What really matters to 6-year-old Jose Carlos Prieto Sosa is that God is there at night to protect him from vampires in his room. "God loves me. He's my friend," he said. "I want God to sleep by my side."
And what matters to 86-year-old Conchita Reyna, who remembers the days when people would throw eggs as she walked into church, is that God was with her the night before, when she held an ice pack to her head all evening because neither the government nor the church had medicine for her migraine headaches.
The tiny woman, who kisses churchgoers on the cheek and remembers the days before the revolution when "the church was everywhere," is still amazed she lived to see the pope's visit.
"It was a very big thing. I never believed he would come, never, never," she said. "Before, we would never have people come to church. They were afraid. Now, the churches are filled."
The task facing the church, its leaders say, is to find new ways to expand its influence amid this uneasy coexistence between religion and government.
No one expects any major breakthroughs.
"The only independent institution in this country is the Catholic Church," said Jorge Luis Duran, director of Caritas in Matanzas province, "and for the government this is unacceptable."