She asked the French to reflect on why the controversial "marriage for all" law - passed only 11 days earlier - had provoked such a "torrent of hatred, violence and division when it is simply to allow a few of our fellow citizens to live their love in broad daylight".
The law, the key social reform of Hollande's presidency to date, provoked unexpectedly fierce debate in a country that prides itself on being a beacon of human rights.
Opponents of the law, which legalises same-sex marriage and adoption, staged mass protests on a scale not seen in decades. The final major protest saw more than 150,000 people march through Paris on Monday and resulted in 293 arrests after clashes between riot police and diehard opponents.
Moved to tears yesterday, Autin, the regional Lesbian and Gay Pride president, said this first marriage proved that "love has triumphed over a part of hatred".
Referring to a 30 per cent rise in homophobic attacks in recent months, he quoted Martin Luther King by saying: "It may be true that the law cannot make a man love me, but it can keep him from lynching me."
Boileau added: "We have had to live with this hatred for months and now we are going to turn the page."
Security was tight with about 100 police officers posted around the building and another 80 waiting in the wings. In the event, only a handful of anti-gay marriage protesters tried to penetrate the town hall with blue flares, but were swiftly arrested.
The few jeers and boos heard when the couple arrived were soon drowned out by well-wishers who filled up Montpellier's main square. After exchanging wedding rings, the couple kissed to general applause.
The hardline Catholic group Civitas criticised the ceremony as lifting the lid on a "Pandora's box" towards incest and polygamy.