The pope was chosen in a lottery among three other Coptic church leaders Nov. 4 to replace Pope Shenouda III, who died in March.
Hundreds of Egyptian Christians, state officials and international dignitaries were on hand at the cathedral to observe the inauguration, Ahram Online reported.
"He will pray for the entire leadership and will obey the words of God, " one church official said at the ceremony.
Egyptian President Mohamed Morsi was not at the event, but sent representatives in his place. Prime Minister Hisham Qandil arrived 2 hours after the start of the ceremony, Ahram Online reported.