"Marwan Charbel has signed the civil marriage contract of Nidal Darwish and Kholoud Sukkarieh, the first Lebanese couple to celebrate a civil union" on home soil, the National News Agency said.
Lebanon has a population of some four million people with Muslims -- Sunnis and Shiites -- making up the majority but with a Christian minority of around 35 percent and a sprinkling of other religions.
Sukkarieh and Darwish's campaign to register their marriage began more than a year ago. It started in secret to sidestep political obstacles, but in recent months their story triggered a massive debate over whether civil unions should be allowed in Lebanon.
Most faiths have their own regulations governing marriage, divorce and inheritance, and mixed Christian-Muslim weddings in Lebanon are discouraged unless one of the two converts.
Despite some clerics and politicians rejecting Darwish and Sukkarieh's union, public figures including President Michel Sleiman have been overwhelmingly supportive of the step.
"Congratulations on the registration of Kholoud and Nidal's marriage contract," Sleiman posted on Twitter on Thursday.
Speaking to private news network LBC, Darwish described the registration as "the first victory for the civil state in Lebanon, the state we all dream of".
He echoed calls for a state for all its citizens in Lebanon, rather than a nation fractured along sectarian lines.
"I am very happy today, and I never had any fear that my marriage to Nidal would not be legal," Sukkarieh told LBC.
"This is Lebanon's first historic step" towards institutionalising civil marriage, she added.
Sukkarieh is four months pregnant, the broadcaster reported.
The couple's efforts to legalise their civil union "is a good thing for us all" in Lebanon, their lawyer Talal al-Husseini said.
"We have here a situation where something could have been legal all along, but where the right to practise civil marriage was blocked," he told AFP.
Lebanese authorities have all along recognised civil marriages registered abroad, and it has become common for mixed-faith couples to marry in nearby Cyprus.
Rather than follow that route, however, Sukkarieh and Darwish decided to work with legal advisers to try to create new jurisprudence, despite no history of civil marriage in Lebanon.
Both had their sect, Shiite and Sunni Muslim, legally struck from their "sejel an-nufoos" or family register, to be wed as a secular couple under an article dating from the 1936 French mandate that makes reference to civil unions.
"They decided to stand before the Lebanese state as citizens, not as members of this or that sect," said Husseini.
"Now that they have established this precedent, there is no going back. It is a big success, and it gives the right to others to follow suit," he added.