Pope Tawadros II broke a ban on pilgrimages to take part in the funeral at a church at the Holy Sepulcher compound, where the Coptic church has maintained a presence since early Christianity.
The travel ban to Israel was imposed by Tawadros's predecessor, the late Shenouda III, who opposed the normalization of ties between Egypt and Israel.
A 1979 Egyptian-Israeli peace treaty ended hostilities between the two neighbors. But anti-Israel sentiments still run high in Egypt and many there have accused Tawadros of betrayal.