Francis, leader of the world's 1.2 billion Catholics, said he hoped for "peace to those who have lost a person dear to them as a result of brutal acts of terrorism".
Religious ceremonies in Germany were heavy also with the weight of Monday's attack, which was claimed by the Islamic State group.
"Christmas this year carries a deep wound - we are celebrating this festival in a different way this year," said Gebhard Fuerst, bishop of Rothenburg in the southeast.
But Baden bishop Jochen Cornelius-Bundschuh offered a note of hope.
"At Christmas, a light shines in the world - it shines in powerful darknesses like those we have seen in recent years with the horror of war, civil war and terrorist attacks," he said.
The country's interior minister Thomas de Maiziere praised the public's reaction as "brilliant".
"I am impressed by the determination... the Germans remain unshakeable," he told the Bild newspaper.
Europe has ramped up security for the holiday just days after the truck attack that left 12 dead at a Berlin Christmas market on Monday.
In Milan, where suspected Berlin attacker Anis Amri was killed in a police shootout on Friday, there was a heavy police presence around the cathedral.
The entrance has been protected by concrete barriers since the Berlin attack.
In France, where Berlin has raised grim memories of the jihadist truck rampage in June that left 86 people dead, 91,000 members of the security forces have been deployed to guard public spaces including churches and markets over the weekend.
80-year-old Pope Francis also used his address to urge peace in the Middle East and called for guns to fall silent in Syria, saying "far too much blood has been spilled" in the nearly six-year conflict.
A crowd of 40,000 gathered to hear the Pope's message in the square below the balcony of Saint Peter's Basilica. The square, despite the sunny weather, was far from full.