He was ordained a priest of the Archdiocese of Paris on 19 April 1930 by Archbishop Alfred-Henri-Marie Baudrillart, rector of the Institut Catholique. From 1931 to 1934, he served as secretary to Pierre-Marie Gerlier, Bishop of Tarbes-et-Lourdes. He taught at the Clermont seminary and the Catholic University in Lyon, serving as vice-rector of the latter from 1942 to 1950. At the start of 1950 he was incardinated into the Archdiocese of Lyon.
On 17 December 1959, he was named Coadjutor Archbishop of Lyon and titular archbishop of Bosporus. He succeeded Cardinal Gerlier as Archbishop of Lyon on 17 January 1965.
He was named Prefect of the Congregation of the Council (later renamed the Congregation for the Clergy) on 7 April 1967. Two years later, on 2 May 1969, he was named Cardinal Secretary of State[4] as part of Pope Paul's program to internationalize the Roman Curia. Though Villot told reporters "I have long been a Roman at heart", his appointment was resented by the Italians though without public conflict.[2] Pope Paul underscored his stance by adding to Villot's portfolio in May 1969, naming him head of the Section if the Secretariat of State responsible for foreign affairs, expanding his control over broader curia by making him President of the Pontifical Commission for Vatican City State and of the Administration of the Patrimony of the Apostolic See.[5]
Villot was named Camerlengo of the Holy Roman Church on 16 October 1970, the first non-Italian to hold the office in half a millennium, a further testament of Pope Paul's insistence on expanding the role of non-Italians at the highest levels of the Vatican bureaucracy.[2] On 15 July 1971, he was appointed President of the newly formed Pontifical Council Cor Unum, a position he resigned on 4 September 1978, during the brief pontificate of Pope John Paul I.
Pope John Paul I retained Villot as Secretary of State.[7] When Pope John Paul II announced that he would retain Villot as Secretary of State, he made clear the appointment was short-term but also confirmed Villot in his other positions. He noted that Villot himself had suggested that the first non-Italian pope in centuries might want an Italian as his Secretary of State.[8][9] He remained in office until his death in March 1979.[10]
Villot participated as a cardinal elector in both the August and Octoberconclaves of 1978, which elected John Paul I and John Paul II respectively, and presided at the conclaves because he was the senior cardinal bishop in attendance. As Camerlengo he acted as the interim administrator of the Holy See in the interregnums of 1978.[2]