"The DNA test just confirmed that Mourad Gharsalli was shot dead yesterday (Friday)," presidential spokesman Moez Sinaoui wrote in a post on his Twitter account.
The interior ministry had previously said that five "terrorists" were gunned down on Friday in the central region of Gafsa.
Gharsalli, a 32-year-old Tunisian, was one of the leaders of the Okba Ibn Nafaa Brigades, the country's main jihadist group and one the authorities have accused of being behind several recent attacks.
Tunisia has seen a surge in radical Islam since veteran president Zine El Abidine Ben Ali was ousted in a 2011 revolution.
Dozens of members of the security forces have been killed since then in jihadist attacks.