These are the first two children, other than martyrs, to be declared saints by the Catholic church.
The canonisation of Jacinta and Francisco Marto was the high point of the celebrations of the centenary of the apparitions in Cova da Iria and took place at the start of the Mass that the Pope celebrated at an altar in the shrine
The Pope left Fatima just after 14:30 in the Popemobile to go back to Monte Real air base where TAP Portugal had two planes waiting to take him back to Rome.
Vatican spokesman, Greg Burke, said there were over 500,000 people in Fátima to witness the canonisation.
Earlier, Pope Francis had begun his pilgrimage to Fátima with a silent prayer in front of the image of Our Lady of Fatima in the Chapel of the Apparitions.
The Pope arrived at the Chapel of the Apparitions where members of the Catholic Church were waiting for him.
He first went to the image of Our Lady of Fátima, which moments earlier had had the protective glass removed and laid at her feet a bunch of white flowers, a gesture that was applauded by the thousands of faithful in the Fatima sanctuary.
After the ceremony, he went back to the Popemobile and greeted some of the children who were waiting beside the Chapel of the Apparitions.
At 21:30, Pope Francis presided over a candle-lit blessing and prayers at the Chapel.
The Pope was in Fátima for two days to celebrate the 100th anniversary of the ‘Apparitions’ of 13 May 1917 and to canonise the shepherds, Francisco and Jacinta Marto.