"These refugee camps -- so many are concentration camps, crowded with people... because international accords seem more important than human rights," Francis said in impromptu remarks at a ceremony in memory of modern-day Christian martyrs.
Departing from his prepared script and appearing unusually emotional as he spoke, the 80-year-old pontiff said he wanted the woman to be remembered along with all the other martyrs commemorated in Rome's Basilica of St Bartholomew.
He revealed that he had met the woman's husband and their three children during his visit to a refugee camp on the Greek island of Lesbos last year.
"I do not know what happened to him, if he managed to get out of his concentration camp, and get to somewhere else" Francis said.
"He looked at me and said 'Father, I am a Muslim and my wife was a Christian. In our country we were terrorised ... they saw her crucifix and they asked her to throw it away.
"When she refused they cut her throat in front of my eyes. We loved each other so much."
Francis did not reveal the man's nationality but most of the migrants in Lesbos at the time of his visit were refugees from the conflict in Syria and he returned to Rome with three families who had fled the conflict there.
They have since begun new lives in Rome and the pope met Saturday with other refugees brought to Europe by legal routes under the auspices of the Sant'Egidio community.
He told them all that Europe needed to be infected by the generous spirit towards migrants that has been shown by the people of Lesbos and the Italian islands of Lampedusa and Sicily.
"We live in a civilisation that is not having children, but also closes its door to migrants: this is called suicide," he said.
"Let us think about the cruelty afflicting so many people, about the exploitation of those arriving on boats.
"Italy and Greece are providing a welcome but then international agreements mean they cannot move on."
Francis also upbraided the growing number of Italian politicians claiming the country cannot cope with an influx which has seen over half a million migrants arrive on its territory in the last three years.
"If every municipality in Italy took in just two migrants there would be a place for everyone," he said.
Saturday's service at the Basilica located on an island in the Tiber river that separates most of Rome from the Vatican, was also addressed movingly by Roselyne Hamel.
She is the sister of Jacques Hamel, the 85-year-old priest murdered by jihadists last year as he was celebrating mass in his church in Normandy in northern France.
"At his age, Jacques was frail but he was strong in his faith in Christ, strong in his love for the Gospel," Roselyne Hamel said.
Describing her sibling as "a universal brother," she said she was certain his love for humanity would even have extended to his killers.
Other speakers included Francisco Hernandez, a friend of William Quijano, an organiser of "Schools for Peace" in El Salvador and a victim of gang violence in 2009, and Karl Schneider, son of Paul Schneider, a protestant pastor who died in the Nazi death camp at Buchenwald.
The Basilica where Saturday's service took place is home to a large collection of relics of Christian martyrs across the ages, including recently added momentoes of Schneider, Quijano and Hamel.