During its national synod the United Protestant Church of France approved the reform with the backing of 94 members versus three who voted against.
The Church has 250,000 members across France and is the largest Protestant denomination, with most of the country identifying as Catholic.
France legalised gay marriage two years ago and this change by the Church means gay couples can have their marriage blessed in a church, but they can still not get married.
Church leader Laurent Schlumberger said: "The synod has decided to go a step forward in supporting those couples by opening the possibility of holding liturgical celebrations when they are requested.
"It's an option, not an obligation, every pastor and every parish is free to implement this change.
"The decision was adopted overwhelmingly and calmly, and has allowed us to move forward together, even if different positions within our Church remain on this subject."
The Catholic Church and most other Protestant churches in France continue to oppose gay marriage saying it goes against Biblical teachings.