"Never again, Lord. Never again!" he said in the dimly lit Hall of Remembrance in the Yad Vashem Museum which commemorates six million Jews killed by the Nazis in World War Two.
The fourth pope to visit Israel, Francis had earlier become the first to lay a wreath at the tomb of Theodor Herzl, seen as the founder of modern Zionism.
At the request of Prime Minister Benjamin Netanyahu, he also made an unannounced stop at Israel's Memorial to the Victims of Terror. "I pray for all the victims of terrorism. Please, no more terrorism," the pope said at the memorial, which is engraved with the names of Israeli civilians killed mainly in attacks by Palestinian militants.
At Yad Vashem, the pope displayed the type of humility that has become his trademark since being elected pontiff in 2013.
As he was introduced to six survivors of Nazi concentration camps and told of their stories of struggle and near-starvation, he bent slowly to kiss the hand of each elderly person.
He called the Holocaust "a boundless tragedy", adding: "A great evil has befallen us, such as never happened under the heavens."