In 1950, Cardinal Alfredo Ottaviani asked Jelmini to allow Agustoni, whom he had met on several occasions, to work in the Congregation for the Doctrine of the Faith (CDF) while continuing his studies.

Following the Second Vatican Council he helped to coordinate the curial departments engaged in Pope Paul VI's program of liturgical renewal.

[1] On 18 December 1986 Pope John Paul II appointed Agustoni Titular Archbishop of Caprulae and Secretary of the Congregation for the Clergy.

On 2 April 1992 he was appointed Pro-Prefect of Apostolic Signatura, becoming Prefect when created Cardinal-Deacon of Santi Urbano e Lorenzo a Prima Porta on 26 November 1994.

Agustoni resigned as Ottaviani's secretary in 1970 to join the Ecclesiastical Magistrature as Prelate Auditor of the Tribunal of the Roman Rota and there is no evidence to suggest his departure was anything more than a routine change of assignment.