Francis was joined by Armenian President Serzh Sargsyan at a church service in Rome on the centenary of the mass killings of Armenians under Ottoman rule in World War One.
Armenia claims up to 1.5 million people were murdered by Ottoman forces during a genocide.
The country, now Turkey, denies it was genocide and says the number killed is much smaller.
The service was seen as an act of reconciliation between the two countries.
Pope Francis said Ottoman officials were guilty of "systematically planning the annihilation of their brothers" but he stopped short of using the word genocide.
"Let us invoke divine mercy so that for the love of truth and justice, we can heal every wound and bring about concrete gestures of peace and reconciliation between two nations that are still unable to come to a reasonable consensus on this sad event," he said.