Lawmakers approved the law by a 40-38 vote.
This law will allow couples to enjoy almost the same rights as married couples, including financial, social and health benefits provided by the government and legal protection for children, as the Associated Press reported.
By cons, adoption is still not possible despite the fact that a partner can adopt the biological child of the other.
It will be necessary to wait some months before the law applies as it is scheduled to go into effect in January 2016.
"Estonia (has) made a leap toward a society that is freer, more equal and values human rights for all," the Estonian Human Rights Center director, Kari Kasper, said.