A cabinet meeting agreed the borders would be reopened "from midnight," government spokesman Amadou Coulibaly said.
The West African state shuttered its land, sea and air borders on March 22 2020 as the global coronavirus pandemic began to gather pace.
The sea and air borders were reopened after a few months, but the country's land borders with neighbouring Burkina Faso, Ghana, Guinea, Liberia and Mali remained closed.
The policy prompted widespread use of back roads to cross the border.
Coulibaly said, "Today we control the clandestine crossing routes, and we urge all travellers to transit through official crossing points."
The West African state, a regional economic power through its exports of cocoa and coffee, recorded a relatively low toll of Covid fatalities.
According to official figures, 800 people died, in a population of 27 million.