The US granted his request to have his wife artificially inseminated with his sperm while he was still in jail.
Hernandez is one of the Cuban Five, a group of Cubans convicted on spying charges in the US and sentenced to lengthy prison terms in 1998.
Their case long soured relations between the two countries.
Hernandez, who was serving a double life sentence for spying, was hailed as a hero upon his return to Cuba in December.
His frozen sperm was transported to Cuba via Panama.
Pictures of the smiling father holding baby Gema were published in the Cuba's state-run newspaper, Granma.
BBC Cuba correspondent Will Grant says some newspapers have dubbed it a "diplomatic conception" in reference to the unusual co-operation between historic rivals Cuba and the US to grant the couple's wish for children.
US Senator Patrick Leahy, who has long campaigned to restore US relations with Cuba, said he had been approached by Hernandez's wife, Adriana Perez.
Ms Perez told him she feared she was running out of time to have children and asked him to intercede with the US government on her behalf.
According to Senator Leahy, he worked with the Obama administration to arrange the artificial insemination.
On the second attempt, Ms Perez, 44, became pregnant.
Hernandez and two remaining members of the Cuban group were freed on 17 December in return for the release of US contractor Alan Gross from a Cuban prison.
Shortly after the release, President Obama and his Cuban counterpart, Raul Castro, announced plans to restore diplomatic ties frozen since 1961.
The other two members of the Cuban Five had already been freed in 2011 and February 2014 respectively after serving their sentences.
A Cuban secret agent, Gerardo Hernandez, who was released last month by the US as part of a diplomatic thaw with Cuba, has become a father.