"The gratitude of the entire Church goes to those who did everything in their power to save the basilica, even risking their lives," he told tens of thousands of people in St. Peter's Square for his general audience.
Notre-Dame's spire was destroyed and its roof gutted but the bell towers were still standing and many valuable art works were saved after more than 400 firemen contained Monday's blaze.
Addressing French pilgrims and visitors in Rome, the pontiff told them he felt their pain.
"May the Virgin Mary bless and support the work of reconstruction. May it be a harmonious work of praise and glory to God," he added.
The Vatican has said it is willing to offer restoration know-how to help rebuild the fire-damaged landmark.
"We have many relationships with the Louvre, other museums and other institutions of French Christianity. Clearly, we are willing to do anything we can to help," Barbara Jatta, the head of the Vatican Museums, told Reuters.
Jatta and her staff of art historians and restorers have worked on such stone masterpieces as Michelangelo's Pieta and his Sistine Chapel frescoes.
Father Enzo Fortunato, a Franciscan at the Basilica of St. Francis in Assisi who was inside that church when the roof collapsed in a 1997 earthquake, also offered words of encouragement to the French.
"Notre Dame is like Assisi. It will rise again. Our experience showed that through pain and hard work, but above all with solidarity, life can come from destruction," he told Reuters. "Prayer was the weapon that allowed us to never lose hope."
Fortunato and other survivors emerged covered in white dust from the collapse, which killed two monks and two city workers.
The Assisi basilica reopened after two years of painstaking restoration that included piecing together thousands of pieces of ceiling frescoes.
"Assisi and Notre-Dame are both symbols of Christian identity and national identity. Precisely because of this, they offer the strength and courage to be reborn," he said.France hopes Notre-Dame can be restored in five years.