Foreign Minister Urmas Paet and his counterpart from Togo, Robert Dussey, established formal relations between the two nations in New York.
Paet said Estonia is very worried about the spread of the Ebola virus, which is spreading close to Togo.
He said smaller nations such as Estonia and Togo are under-represented on the UN Security Council.
Togo, population six million, was one of the last nations Estonia had not signed diplomatic relations with. Bhutan, Swaziland, Tonga and North Korea are among the remaining 11 countries.