"I declare on this day, January 18, 2015, the end of the end of the Ebola epidemic in Mali," Ousmane Koné said in a statement in which he thanked the country's health workers and international partners for their work to halt the outbreak.
The country "had come out" of the epidemic, confirmed Ibrahima Soce Fall, the head of the Malian office of the United Nations Mission for Ebola Emergency Response (UNMEER).
Countries must report no new cases for 42 days - or two incubation periods of 21 days - to be declared Ebola-free, Al Jazeera reported.
Mali recorded seven deaths caused by the Ebola outbreak that began just over a year ago.
According to World Health Organisation (WHO) data the worst epidemic of the viral haemorrhagic fever on record has killed more than 8,400 people, mostly in neighbouring Guinea, Sierra Leone and Liberia.
At least 21,296 people have so far been infected with the virus, the WHO has said.
Mali's last infected patient recovered and left hospital early last month. At one point health officials had been monitoring more than 300 contact cases.
Mali became the sixth West African country to record a case of Ebola when a two-year-old girl from Guinea died in October. It was close to being declared Ebola free in November before a second wave of infections.