"As I depart from the UAE, I renew my deep appreciation to your highness, the government and the people of the UAE for your warm welcome and generous hospitality", the Pontiff said in a message sent to UAE President Khalifa bin Zayed Al Nahyan.
The Filipino Times newspaper reported that the Mass saw a 120-member choir, composed mostly of Filipinos, with Filipina conductress Joy Santos spearheading the multi-cultural voices who sang hymns in English, Arabic, and Latin.
"Let us pray loudly", Francis said, "because there are children that are hungry, are thirsty, don't have medicine and their lives are in danger".
The pope and the grand imam of al-Azhar signed a historic declaration of fraternity, calling for peace between countries, religions and races, before an audience of religious leaders across the world from Christianity, Islam, Judaism, and other different beliefs.
Some 4,000 tickets had been given to Muslims to attend the mass, according to the local churches.
The UAE is part of the Saudi-led military coalition engaged in the war in Yemen.
Yemen is in the grip of what the United Nations calls the world's worst humanitarian crisis, triggered by the intervention of Saudi Arabia, the UAE and their allies in a civil war between the government and Shiite Muslim rebels.
HH Sheikh Mohamed bin Rashid, Ruler of Dubai, took to Instagram to share photos from the document signing, which he captioned, "UAE today was proud to host the historic meeting of His Holiness Pope Francis and His Eminence Dr. Ahmad Al Tayeb".
"The Lord specializes in doing new things; he can even open paths in the desert", he said at the end of a trip where he met with the grand imam of Egypt's Al-Azhar mosque and U.A.E. leaders.
Vatican officials said before the trip that it was not clear whether the pope would address the subject of the almost four-year Yemen war in public or private during the trip.
The Pope's visit, following an invitation by His Highness Sheikh Mohamed bin Zayed Al Nahyan, Crown Prince of Abu Dhabi and Deputy Supreme Commander of the UAE Armed Forces, will draw attention to the global role of the UAE as an worldwide leader in promoting religious coexistence.
It is the first-ever trip by a pope to the Arabian Peninsula.
That prompted 138 Muslim scholars to write a letter to Benedict and other Christian leaders emphasizing that world peace depended on harmony between the two faiths.
About one million Catholics live in the country, or about one in 10 of UAE residents.