While same-sex couples in the country are not allowed to legally marry in a church, gay and lesbian couples will now be able to mark and celebrate their civil partnerships in a church service - or "blessing" ceremony.
At least one partner must be a member of the Waldensian church however.
Gay blessings have been offered by the church since 2010 on a case-by-case basis, but with this position, the synod formally recognised "the plurality of different models of coexistence and family life in society".
The move follows Italy's adoption in October 2016 of civil unions for gays and lesbians, which came despite the Catholic Church's opposition.
With that legislation, Italy became the last country in Western Europe to legally recognise same-sex relationships.
Founded in the 12th century, the Waldensian Church preached the Christian Gospel in the countryside and was persecuted by the Catholic Church.
The world's oldest Protestant community founded some 350 years before Luther's reformation, Waldensians were repressed by the civil and religious authorities until the middle of the 19th century when modern-day Italy came into being.
The community now numbers between 25,000 and 40,000 believers, mostly in the north of Italy.
Gay marriage blessings are common in Protestant churches in the north of Europe, France, Germany, Spain and Switzerland.