The Holy Father remembered murdered president of the Turkish Bishops' Conference, Bishop Luigi Padovese, before consigning the Instrumentum Laboris on Sunday.
The bishop, who had planned on attending the very celebration the Pope was presiding over, was recalled by the Holy Father for his contributions to the preparation of the working document.
News of his death "shocked all of us," said the Pope.
The Italian-born bishop had been the vicar apostolic to the country for most of the last six years, but his service came to an end when he was killed by his driver, Murat Altun, on Thursday for still unknown motives. International news media have reported that Altun suffered from psychological problems.
After Mass on Sunday, Pope Benedict XVI entrusted the prelate's soul "to the mercy of almighty God, mindful of how committed he was, especially as a bishop, to interreligious and cultural understanding, and to dialogue between the Churches."
He added that the death of Bishop Padovese is "a sobering reminder of the vocation that all Christians share, to be courageous witnesses in every circumstance to what is good, noble and just."