Pope Benedict was greeted by the younger Castro brother and the two men walked through a gantlet of Cuban guards at Communist Party headquarters.
They sat on a pair of overstuffed chairs and conversed for the cameras before meeting privately. Neither the Vatican nor Cuban officials revealed what was discussed.
However, Tuesday morning after praying for political prisoners at the shrine honoring Cuba's patron saint, the Virgin of Charity of Cobre, Pope Benedict appeared on Cuban television making pointed remarks about dissidents who are suffering.
"I have entrusted to the Mother of God the future of your country, advancing along the ways of renewal and hope, for the greater good of all Cubans," the pope said. "I have also prayed to the Virgin for the needs of those who suffer, of those who are deprived of freedom, those who are separated from their loved ones or who are undergoing times of difficulty."
Oddly, just as the pontiff began talking about political prisoners, Cuban TV switched away from showing his face.
In an unusually fast retort, a top Cuban official, Marino Murillo, vice-president of the council of ministers, called a news conference to announce that "in Cuba there won't be political reform."
As the papal motorcade left Revolution Palace Tuesday night following the meeting with Raul Castro, Vatican staff was walking through Wednesday morning's public Mass, making last minute adjustments in the staging.
But even as ABC 7 shot video of the rehearsal for the Roman Catholic religious ceremony, Cuban police seemed troubled by our presence.
There had been speculation that Castro's older brother, Fidel, would also meet with the pope. That did not happen Tuesday.
Venezuelan President Hugo Chavez, who is in Havana undergoing radiation therapy for cancer, did not ask for an audience but would be welcome to attend Mass in the capital's Revolution Square on Wednesday, a Vatican spokesman said.
The pope spent Monday in Santiago in southeastern Cuba. He will celebrate a Mass in Havana on Wednesday before returning to Rome.
Cuba controls media during papal trip
When it comes to the cuban government, there are some things that they do not want the foreign press to see.
No one prevented ABC7 Chicago from taking pictures of a boy jumping into the ocean. Happy Havana. Tourista specials to beam back to viewers in Chicago.
But when ABC7 attempted to shoot video of most anything else, voices would be raised from our flank. And phone calls were made, suggesting Cuba's secret policia wouldn't be far behind.
If they did arrive, ABC7 made sure to be long gone.
As international media arrived in Cuba the past few days to cover Pope Benedict, hoteliers, restaurateurs and retail employees tell ABC7 they received an edict from Cuban government officials: news cameras are not to be permitted to photograph their premises.
Especially sensitive were the slums of Havana. In a city where the majority of residents are equally poor - making $20 a month- that area, off the tourist maps, houses the dirt destitute.
And when it came to Cuba's passion, baseball, another tactic was used. ABC7 wanted to visit with Cuban baseball stars, but the stadium was empty.
Ivan Lopez is a long time announcer in Cuba, Havana's version of Harry Caray.
"It's the same as in Chicago," said Lopez. "Sometime's the Chicago white sox have to go to some other state to play."
Off camera, Lopez told ABC7 a far different story, confirmed by Cuban government sources: during the pope's visit, all games would be moved inland, to small ballparks. Western media would no longer have easy access to interview potential defectors.
The Associated Press contributed to this report.