The latest outbreak was from the same cholera strain found to have been introduced in Haiti by Nepalese UN peacekeepers, unleashing an epidemic in 2010 that has killed some 7,900 people.
Miriam Rodríguez, who lives in the Havana neighborhood most affected by the outbreak, said her son, Ubaldo Pino, a 46-year-old barber, succumbed to the disease on January 6.
"He died of cholera and that is what is on his death certificate," she told AFP. Authorities have not officially confirmed the cause of his death.
The Health Ministry said the outbreak was detected in the Cuban capital, a city of 2.2 million people, on January 6 after a surge in cases of acute diarrhea.
It said 51 cholera cases had been confirmed.
The Pedro Kouri Institute of Tropical Medicine traced the disease back to the same strain of cholera that caused last year's outbreak in the city of Manzanillo, 800 kilometers (480 miles) east of Havana in Granma province.
That outbreak, which hit in July and was declared eradicated August 28, claimed the lives of three people and infected 417.
It was the first time cholera had been reported on the Caribbean island since 1882.
The Health Ministry said the Havana outbreak "is in a phase of extinction."
It said the cholera was "generated by a food vendor, an asymptomatic carrier of the disease, contracted earlier in other regions of the country," the Health Ministry said.
It first appeared in a working class district called Cerro situated in the center of Havana, between the Plaza of the Revolution and the city's main baseball stadium.
Rumors of a cholera outbreak spread in recent days after doctors and nurses began going door to door in certain neighborhoods to distribute medicines to residents.
"They came to all the houses and said, 'Are you allergic to penicillin?' And they gave us three Doxycycline pills to take, but wouldn't tell us anything. I asked them if it was cholera, and they laughed but didn't tell us anything," a woman told AFP.
The Health Ministry called on the public to pay increased attention to hygiene, urging frequent hand-washing, the drinking of chlorinated water, and careful cleaning and cooking of food.
Preventive measures also were being taken at Havana clinics and schools, various sources told AFP.
Rodriguez praised the medical attention her son received, but said he had been weakened by alcoholism.
"If he had been a strong person he would have been saved," said Yanicet Pino, the victim's sister, who said Pino first presented symptoms on December 22 but refused to see a doctor.
The outbreak comes at the height of the tourist season in Cuba, which runs from December to April, when planeloads of travelers descend on the island from Canada, Europe and Latin America. Nearly three million tourists visited Cuba last year.
Cuba was a Spanish colony when the last major cholera epidemic swept the island from 1867 to 1882, leaving nearly 6,000 dead, according to the Medical Sciences Information Center in the western province of Matanzas.
Cuban doctors have gained experience treating the disease in Haiti, which suffered a cholera epidemic that originated in the Artibonite river valley near a base for UN peacekeepers from Nepal.
A 2011 study published by the US Centers for Disease Control and Prevention found that the cholera strain was brought to Haiti by the Nepalese peacekeepers.
The outbreak in Haiti, which had never had a recorded case of cholera, has since spread to Cuba, the Dominican Republic, Venezuela and the United States.
The cholera strain found in Haiti - V. cholerae El Tor 01 - was found to bear a strong relationship to a cholera strain isolated in Bangladesh. It is the same strain identified in the Cuban outbreaks.
Cuban scientists have been working in recent years to develop a vaccine against cholera, which causes serious diarrhea and vomiting, leading to dehydration.
It is easily treatable by rehydration and antibiotics, but the ailment can be fatal if not addressed quickly enough.