Diaz-Canel earlier called for his supporters to take to the streets after accusing the US and enemies of the Cuban Revolution of trying to destabilise the Caribbean nation following large-scale protests.
"There is a group of people ... hired by the US government, paid indirectly through US government agencies to organize this kind of demonstrations," he told his supporters in an address.
The Sunday protest was the biggest anti-government protest in recent years in Cuba. Thousands of people gathered to express dissatisfaction with what they believe are lack of freedom and degrading economic situation in the country. Some protesters demanded that free elections be held, local media reported.
In one of the cities, protesters and counter-demonstrators clashed and began to throw stones at one another. Protesters have also reportedly looted a store and turned over several cars. There were no reports of further incidents or people sustaining injuries.