This event, was organized with the goal of offering "a propitious occasion for reflection and prayer, as well as an occasion for encounter and reconciliation, in a spirit of respect and trust, to those who in this moment have the mission and the responsibility to work for a future of peace and prosperity for the South Sudanese people", said the Vatican.
He said: "I am asking you as a brother to stay in peace".
Pope Francis will give a speech at the end of the retreat on Thursday afternoon. Two years later, South Sudan plunged into its own intermittent civil war, with some 400,000 people killed and almost a third of the population uprooted.
The Vatican, together with the South Sudan Council of Churches and the Rome-based Sant' Egidio global peace group, brought the leaders together for prayer and preaching inside the pope's residence in an attempt to heal divisions.
Pope Francis knelt and seemingly kissed the feet of leaders of war-torn South Sudan, President Salva Kiir and rebel-turned opposition leader Riek Machar, as he pleaded with them not to let blood flow in their home country during a two-day retreat at the Vatican.
Sudan, which is predominantly Muslim, and South Sudan, predominately Christian, fought each other for decades before the south became independent in 2011.
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The arch-rivals last saw each other in October previous year, shortly after the signing of a power-sharing deal, when Machar made a brief return to Juba for the first time since fleeing on foot in a hail of gunfire in July 2016. "In other words, He will ask us to render an account not only of our own lives, but the lives of others as well", the pope said. Pope Francis, Grand Imam of Egypt Kiss In UAE, Call For World Peace; See Pic.
"We have clearly heard the cry of the poor and the needy; it rises up to heaven, to the very heart of God our Father, who desires to grant them justice and peace", he said. The leaders will live there and eat together during the retreat.
The retreat is the brainchild of Justin Welby, head of the Anglican communion, the Vatican Secretariat of State Pietro Parolin, and Rev John Chalmers, former Moderator of the Presbyterian Church of Scotland, who were all present at the meeting. "Your people today are yearning for a better future, which can only come about through reconciliation and peace".
Pope Francis told them how he learned last September that a peace agreement for the country had been signed and congratulated political leaders for "having chosen the path of dialogue".