Five people, including a rabbi from London, were killed when two Palestinians stormed the building with knives and axes.
The suspects were shot dead.
Francis used his weekly General Audience to condemn the attack and urge Israel and the Palestinians to take "courageous" steps towards peace.
He said there had been an "alarming increase in tensions" in the Holy Land and that he was praying for all involved.
Urging an end to the "spiral of hatred and violence" he said both sides had to "take courageous decisions for reconciliation and peace".
He added: "To build peace is difficult, but to live without peace is a torment."