In his message, Pope Francis gave separate greetings to the Egyptian government and to President Abdel-Fattah el-Sisi, who attended the ceremonies.
The inauguration ceremonies began at the complex's convention center. Various artists performed Islamic chants and Christian hymns. A children's choir sang about Egyptian unity amid religious difference, as did the popular singer Angham.
Pope Tawadros toured the mosque with President El-Sisi, Palestinian President Mahmoud Abbas and other local and international leaders.
"This is a day of joy as we see our beloved country write a new page in the history of civilization," the Coptic pope said.
"Today we celebrate an unprecedented occasion where the minarets of Al-Fattah Al-Alim Mosque are embracing those of the Nativity of the Christ Cathedral, opening a new horizon for our beloved country on this happy occasion, achieved through the Egyptian people's donations and efforts with sincerity and love."
"As an Egyptian citizen, I am happy to stand in the mosque to celebrate its opening with my Muslim brothers," he continued, praising el-Sisi's fulfillment of his promise to build the mosque and the cathedral.
"We pray for our unity to continue as the world witnesses such tolerance and love in our country, God bless you all, long live Egypt," he said.
During the dedication of a plaque outside the church, Muslim cleric Sheikh Ahmed al Tayyeb of Al-Azhar Mosque, a leading Sunni institution, said the joint inauguration is "the embodiment of the soul of brotherhood and love." He said Islamic law requires safeguarding Christian and Jewish houses of worship just as mosques are protected.
After entering the cathedral, el-Sisi said the occasion sends the message "that we will not allow anybody to come between us." He voiced dislike for calling conflicts "sectarian strife," because "Muslims and Christians in Egypt are one, and will stay one."
He said the event "represents a tree of love which we have planted together, but this tree still needs attention and care so that its fruit reaches from Egypt to the whole world."
"Strife will not end, but God saved Egypt and he will continue to do so for the sake of its people," the president said. He discussed the 2013 attacks on Egyptian churches, saying Pope Tawadros' words helped the country repair the damage and build new projects.
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El-Sisi, a former general, became president in the 2013 elections following a military coup against a government led by the Muslim Brotherhood. He was re-elected in 2018 but his government's human rights record has faced strong criticism due to its treatment of its political opponents.
The dedication event took place under significant security. A policeman was killed trying to defuse an explosive device near a church in a Cairo neighborhood late on Saturday. The explosion wounded two policemen, including the bomb squad commander, BBC News reports.
In April 2017 Pope Francis traveled to Cairo and appeared in public with Pope Tawadros II and other religious figures. Pope Francis honored various Coptic martyrs during this visit, and declared that the sufferings of the Copts "are also our sufferings."