The four-hour long ceremony at St Mark's Cathedral was looked on by Coptic Orthodox clergy from around the world, including the head of the Coptic Orthodox Church in the UK, Bishop Angaelos.
Also in attendance were Egyptian Prime Minister Hisham Qandil and other politicians.
Pope Tawadros II did not give an address but a short speech was read out on his behalf, in which he pledged to work for the good of Egypt, Muslims and Christians alike.
He succeeds Pope Shenouda III, who died in March.
Pope Tawadros II was selected last month in an altar ballot and takes on leadership of the Church at a time of increasing discrimination against Christians in Egypt.
Speaking from Cairo, Bishop Angaelos was optimistic.
"It is wonderful to be part of this historic moment, seeing the jubilation on the faces of those in the cathedral as our new father and shepherd was enthroned," he said.
"Our prayers are with His Holiness Pope Tawadros II, asking for God's guidance and grace upon him as he enters into this new stage of service, aiding the Coptic Orthodox Church in its continued mission to be light and salt in Egypt and throughout the world."