It was not initially clear why the trip was cancelled but Vatican spokesman Greg Burke told Reuters it "was not for this year" but did not hint on any future schedule.
A Church source said one reason for the cancellation was that a team from the Vatican was not able to secure guarantees that people of both ethnic groups would be able to attend a papal Mass of reconciliation. Vatican sources have also cited insecurity.
The world's youngest country gained its independence from Sudan in 2011. It has been war-torn since a political struggle in 2013, led to fighting, often along ethnic lines, resulting in as many as 300,000 being killed and 3 million displaced.
While the trip to the oil-producing African country was never announced officially by the Vatican, some Church leaders in the country including Bishop Erkolano Tombe country said they had expected Pope Francis would visit the capital, Juba, in October.
The trip was to have lasted only one day with the Pope flying in after spending a night in another African country. It also emerged that the head of the Catholic Church said he wanted the Archbishop of Canterbury, Justin Welby, to accompany him to South Sudan, in an effort to promote unity in the mostly Christian country.
Pope Francis has said several times he wishes to visit the country but the war, between forces loyal to President Salva Kiir and others loyal to his former deputy Riek Machar, means finding the right time and putting in adequate security is difficult.
