St Mark’s cathedral was packed with mourners paying their respects to the 88-year-old pope who died on Saturday.
He was the spiritual leader of Egypt’s Copts, who make up 10% of the country’s population and are the Middle East’s largest Christian community.
Pope Shenouda’s body was then flown to the Nile Delta northwest of Cairo and buried in a remote desert monastery.
Thousands of people greeted the motorcade carrying his body when it arrived just before sunset, and military police struggled to control the mourners trying to get into the monastery.
The patriarch spent more than three years in exile there in the 1980s when the late Egyptian President Anwar Sadat accused him of fomenting sectarian strife.
Two months ago he asked to be interred at St Bishoy monastery on his death – he was laid to rest in a white marble tomb with a cross on top.
The ceiling of the chamber is covered with pictures of Jesus Christ, the Virgin Mary and saints, and it also has small windows to let in some light.
Copts were given time off work to prepare for the funeral, and a national day of mourning has been declared.
Tens of thousands of people queued to see Pope Shenouda, whose body had been on display in the cathedral since his death.
Dressed in embroidered vestments and a golden mitre and holding a gold-tipped staff, his body was laid in a coffin before being placed on a ceremonial throne.
“The Holy Pope was able to gain the love of even those who held different opinions and I believe this will be a difficult thing to replace,” said a mourner named as Samir.
“But God protects the Church and he will find a suitable patriarch.”
Thousands of mourners who were unable to get into the cathedral followed the service on a huge television screen outside.
The BBC’s Jon Leyne in Cairo says the massive crowds bear witness to the huge love and respect for Pope Shenouda.
As the white coffin was carried out from the cathedral there were almost hysterical scenes, with some women wailing and fainting.
The Pope was seen as a leader who did his best to protect Coptic Christians at a time when Islamism was on the rise, our correspondent says.
Read More and watch the video at: http://www.bbc.co.uk/news/world-middle-east-17437325