The doctors are to receive increased allowances as negotiations over other issues continue.
The doctors have been demanding higher wages and better working conditions and say more doctors need to be hired.
About 2,500 public health institutions were affected by the strike.
A number of patients are reported to have died from a lack of medical care during the walkout.
"We are grateful that this dark page in the history of our country has come to an end," Health Minister Cleopa Mailu said at the signing of the deal.