The Council was presided over by Eutychius, Patriarch of Constantinople, assisted by the other three eastern patriarchs or their representatives. Pope Vigilius was also invited; but even though he was at this period resident in Constantinople (to avoid the perils of life in Italy, convulsed by the war against the Ostrogoths), he declined to attend, and even issued a document forbidding the council from preceding without him (his 'First Constitutum'). For more details see Pope Vigilius.
The council, however, proceeded without the pope to condemn the Three Chapters. And during the seventh session of the council, the bishops had Vigilius stricken from the diptychs for his refusal to appear at the council and approve its proceedings, effectively excommunicating him personally but not the rest of the Western Church. Vigilius was then imprisoned in Constantinople by the emperor and his advisors were exiled. After six months, in December 553, he agreed, however, to condemn the Three Chapters, claiming that his hesitation was due to being misled by his advisors. His approval of the council was expressed in two documents, (a letter to Eutychius of Constantinople on 8 December 553, and a second "Constitutum" of 23 February 554, probably addressed to the Western episcopate), condemning the Three Chapters, on his own authority and without mention of the council.
In Northern Italy the ecclesiastical provinces of Milan and Aquileia broke communion with Rome. Milan accepted the condemnation only toward the end of the sixth century, whereas Aquileia did not do so until about 700. The rest of the Western Church accepted the decrees of the council, though without great enthusiasm. Though ranked as one of the ecumenical councils, it never attained in the West the status of either Nicaea or Chalcedon.
In Visigothic Spain (Reccared having converted a short time prior) the churches never accepted the council; when news of the later Third Council of Constantinople was communicated to them by Rome it was received as the fifth ecumenical council, not the sixth. Isidore of Seville, in his Chronicle and De Viris Illustribus, judged Justinian a tyrant and persecutor of the orthodox and an admirer of heresy, contrasting him with Facundus of Hermiane and Victor of Tunnuna, who was considered a martyr.
Despite the conflict between the council and the pope, and the inability to reconcile Chalcedonians and non-Chalcedonians, the council still made a significant theological contribution. The canons condemning the Three Chapters were preceded by ten dogmatic canons which defined Chalcedonian Christology with a new precision, bringing out that God the Word is the one subject of all the operations of Christ, divine and human. The 'two natures' defined at Chalcedon were now clearly interpreted as two sets of attributes possessed by a single person, Christ God, the Second Person of the Trinity. Later Byzantine Christology, as found in Maximus the Confessor and John of Damascus, was built upon this basis. It might have proved sufficient, moreover, to bring about the reunion of Chalcedonians and non-Chalcedonians, had it not been for the severance of connections between the two groups that resulted from the Muslim conquests of the next century.