"The only fanaticism believers can have is that of charity", the pope said at the service.
Pope Francis demanded that Egypt's Muslim leaders teach a rejection of violence in God's name during a delicate visit Friday to the Arab world's most populous country, and he strongly backed its uncompromising crackdown on political Islam and militancy.
Faithful wait for the arrival of Pope Francis at the Air Defense Stadium in Cairo.
On Saturday, the crowd cheered and released yellow and white balloons as Francis lapped the Cairo stadium in a golf cart, waving to onlookers as a chorus sang a joyous hymn.
Egypt has around 272,000 Catholics and 213 parishes out of a total population of almost 89 million.
Egypt's Coptic Christians have repeatedly been targeted in recent deadly attacks, including ones carried out by ISIS.
Worshipers old and young, nuns and priests, had been bused in under tight security with Egypt under a state of emergency following the church bombings.
On Saturday, Francis also repeated his claim that some migrant holding centers in Europe amount to "concentration camps", even after Jewish groups proposed he stop using the term.
Pope Francis also met Christian and Muslim leaders in Egypt during his visit.
As he has on other occasions, Francis called for ecumenical relations rooted in friendship and common efforts, rather than a merely abstract theological dialogue - a "static ecumenism", he said, "doesn't go anywhere".
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"The main aspect of this visit is that we have now to decide, if we need and want this religion, to look into the past, and study the real religion, not what people say about it".
The mass came on the second and last day of Francis's visit, which saw him plead for tolerance and peace on Friday as he visited a Coptic church bombed by IS in December. She said her Muslim friends and colleagues were very apologetic and supportive after the bombings on Palm Sunday.
"But I would say, Mr President, please see to it there is no war, because my region will suffer immensely".
"Pope Francis is a man of peace and his manner of talking and acting shows that he feels what's happening in the Middle East will bring something new, a new spirit, I hope for this". In this regard, we are encouraged to engage in a deeper study of the Oriental and Latin Fathers, and to promote a fruitful exchange in pastoral life, especially in catechesis, and in mutual spiritual enrichment between monastic and religious communities.
Ibrahim Morgan, a parishioner at St. Joseph's Catholic Church in Cairo, told ABC News he now worries about his family when they attend church and feels his Christian community is caught in the fight against Islamic extremism. "With the assurance of my prayers, I invoke upon the nation the divine blessings of peace and joy". "It's very tough and we're having many problems in this fight because it's a battle fought with arms, ideas, religion".
A refugee from South Sudan who teaches fellow refugees at a Catholic school in Cairo, Bolden called Francis "the pope of refugees".
"He is not afraid", Morgan said.
The pope also met with Egyptian President Abdel-Fattah el-Sissi during his stay.
There, he warmly embraced Sheikh Ahmed el-Tayeb, Al-Azhar's grand imam who hosted the pope and other senior Muslim and Christian leaders, students and scholars at a peace conference in a hall featuring a mock-up of the famous Al-Azhar mosque, complete with faux windows and flooded with purple lights.
Following a joint signing of an agreement on the rules of baptism in the Catholic and Coptic churches - which will mean that the Coptic Orthodox Church will now recognize Catholic baptisms - Alexandria's Pope of the Coptic Orthodox Church Tawadros II offered Pope Francis a wooden Coptic-style cross.
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