"I declare this day... the end of the epidemic of the Ebola virus in Mali," said Ousmane Kone.
The last Ebola-infected patient in Mali recovered and left hospital in early December.
Latest figures show the three West African countries worst affected have all seen a decline in new Ebola cases.
Sierra Leone and Guinea both recorded the lowest weekly total of confirmed Ebola cases since August, according to UN figures on Thursday.
Liberia, which reported no new cases on two days last week, had its lowest weekly total since June.
The overall death toll has reached 8,429 with 21,296 cases so far.
Mali recorded its first case of Ebola in October, when a two-year-old from Guinea fell ill and died.
At its worst, there were 300 contact cases under investigation in the country.
But the country has now "come out" of the epidemic, said Ibrahima Soce Fall, the head of the Malian office of the United Nations Mission for Ebola Emergency Response (UMEER).
The incubation period for Ebola is 21 days, and countries must be free of new cases for two consecutive incubation periods, 42 days, to be declared free of the virus.
Ebola basics: What you need to know
Mali's health minister says the country is now free of the Ebola virus, after 42 days without a new case of the disease.