The official Granma newspaper said the Cuban capital was hit last afternoon by a line of severe thunderstorms packing winds of up to 98 kilometers per hour.
The island's civil defense command said the victims included a 77-year-old woman who drowned in flood waters that swept parts of Old Havana.
The newspaper also said a 23-year-old man was electrocuted by a falling powerline.
State-run television also reported the death of a 43-year-old lawyer.
The storm also toppled trees, ripped away roofs and damaged walls.
Three buildings collapsed, and 24 other structures suffered damage, Granma said.
Building collapses are not uncommon in Old Havana where housing stock is densely inhabited and in poor condition.
An estimated 10,000 people were forced to leave their homes, to be taken in by family, friends or at three shelters opened in the city, the civil defense agency reported.
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