The two men - Angel Moya and Guido Sigler - had refused a government deal to go into exile and insisted on staying in Cuba, along with nine other dissidents who remain in Cuban jails nearly seven months after the government agreed in principal to free them.
Under the agreement announced Friday, Moya will stay in Cuba while Sigler "has indicated a desire to go to the United States," church spokesman Orlando Marquez said in a statement.
Sigler arrived at his home in a village near the central city of Matanzas on Friday afternoon, said Elizardo Sanchez, a well-known human rights activist on the island.
Gloria Berbena, a spokeswoman for the U.S. diplomatic mission in Havana, said American consular officials had been in contact with Sigler's family about his case, but would not comment specifically on his status.
"We are in touch with his family about what his wishes might be," she told The Associated Press. "We are absolutely ready to work with them on that."
Moya, who was serving a 20-year sentence for treason and other charges, is the husband of Bertha Soler, one of the leaders of the Ladies in White opposition group. Sigler, who was sentenced to 25 years in jail, is the brother of another dissident who has already been released.
"I am happy, as it is good news," Soler told the AP moments after learning her husband would be freed. "But I am not totally satisfied because of the government's drip-drip approach" to letting the dissidents out.
She said several of the other prisoners are not in good health and should also be freed immediately.
Cuban President Raul Castro agreed in July to free all 52 prisoners remaining from the 2003 sweep, which targeted peaceful activists, social commentators and opposition leaders. Roman Catholic Cardinal Jaime Ortega said at the time that the deal called for the men to be out within four months, or by November.
Authorities quickly released 41 of the men, sending all but one of them into exile in Spain, along with their families. But the process had ground to a halt in recent months, as those who remained behind bars refused to leave Cuban soil, a direct challenge to the government.
Some have also vowed that they will continue to press for democratic political change the moment they leave jail.
Still, pressure has been building on the government to make good on the agreement.
Last week, the wife of Diosdado Gonzalez, another of the 11 remaining 2003 prisoners, began a hunger strike to demand her husband's freedom. The protest was joined from behind bars Tuesday by Gonzalez and another political prisoner.
The Cuban government had no immediate comment on the latest releases. Authorities rarely acknowledge the dissidents, except to say that they are all common criminals and stooges paid by Washington to destabilize the island.
Associated Press writer Andrea Rodriguez contributed to this report.