"We are all aware that this meeting is something altogether special and in some sense unique, since it is neither an ordinary bilateral or diplomatic meeting between the Pope and Heads of State, nor an ecumenical initiative involving representatives of different Christian communities," Pope Francis said.
"The purpose of this retreat is for us to stand together before God and to discern his will," he continued. "It is to reflect on our own lives and the common mission the Lord has entrusted to us, to recognize our enormous shared responsibility for the present and future of the people of South Sudan, and to commit ourselves, reinvigorated and reconciled, to the building up of your nation."
Francis expressed his "spiritual closeness" with the all of the South Sudanese people, particularly refugees and the sick.
South Sudan's civil war has left 2.1 million people internally displaced, with another 2.5 million refugees, according to the United Nations.
"May the Merciful God touch the heart of every man and every woman in South Sudan, fill them with his grace and blessings, and bring forth rich fruits of lasting peace, even as the waters of the Nile, flowing through your country, bring life and abundant growth," Pope Francis said.
Pope Francis confirmed his "desire and hope" to visit South Sudan soon, adding that this future visit would be together with Welby and and the former Moderator of the General Assembly of the Church of Scotland.
A prior trip to the war torn country with Welby was cancelled in 2017 due to security concerns.
"Upon all the Christians of South Sudan who, in helping those in greatest need, bind up the wounds of Jesus' body, I implore God's abundant graces and assure them of a constant remembrance in my prayers," Pope Francis said.
"Peace is the fundamental condition for ensuring the rights of each individual and the integral development of an entire people. Jesus Christ, whom God the Father sent into the world as the Prince of Peace, gave us the model to follow," he said.
"Peace is the first gift that the Lord brought us, and the first commitment that leaders of nations must pursue."