The stoppage was called by the country's two main health unions, demanding raises for staff and jobs for contract workers, though a skeleton emergency service was maintained.
"The demand for strike action is lifted because we are satisfied," said Yossouf Maiga, a senior official with one the unions, adding that eight of nine demands had been met.
Government spokesman and commerce minister Abdel Karim Konate confirmed to AFP the strike was over.
"The strikers and the government have reached agreement," he said.