He was consecrated Bishop by Eugene Cardinal Tisserent, Secretary of the Sacred Congregation for the Oriental Churches, on 9 November 1950 at St. Theresia's Church Rome and was installed in Palai Cathedral by the Most Rev.
Bishop Vayalil was a member of the Preliminary Commission instituted for the Second Vatican Council to prepare the scheme for the section on 'Universities and Seminaries'.
Chicago's De Paul university conferred upon him in 1966 the honorary Degree of Doctor of Laws (L.L.D.
In 1969 he participated in the extra ordinary Synod of Bishops held in Rome.
On the acceptance of his resignation he handed over the charge of the diocese to his successor Mar Joseph Pallikaparampil on 25 March 1981.