The Holy See and Malta have agreed to a revision of the marriage agreement, which will be signed tomorrow, according to the Curia.
Just weeks after the general election, the Labour government had sent a note verbale to the Holy See requesting talks to amend the 1992 document.
When a Nationalist government introduced the agreement it laid down that civil marriages were conditional to procedures by the Church Tribunal if one of the spouses opted to annul the marriage in that court, giving supremacy to the Church.
But the Labour government argued that the civil courts should be supreme, in line with the separation of Church and State.
During a meeting with the Pope in June, Prime Minister Joseph Muscat said the agreement was often abused by couples to vindictively delay the separation process, not through religious conviction.
Foreign Minister George Vella and Nuncio Aldo Cavalli led the talks that began soon afterwards.