The talks focused on cooperation in international, political and economic issues, according to the local media on Saturday.
Cuba is the second leg of Zarif's three-nation tour to Latin America.
First, he visited Venezuela. After Cuba, the foreign minister is to travel to Bolivia.
In the Havana meeting, the two sides expressed support for the Palestinian cause, and called for fostering cooperation in biotechnology and nanotechnology.
Earlier, Zarif visited medical and pharmaceutical centers in Havana and listened to explanations of the heads of the two centers about the progress made in the production of various vaccines, especially the COVID-19 vaccine.
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