The court rejected an appeal by the defendants, confirming 14 year jail sentences for them, Ahram reported.
Tuesday's verdict comes after 23 defendants, including the nine who appealed, were sentenced to 14 years in prison while eight others were acquitted by a Giza criminal court in 2015.
The general prosecution charged the men with organising an assembly to commit murder and killing Shehata and three of his sons. Not less than 3,000 angry locals were involved in the attack.
According to the Egyptians Against Religious Discrimination group, the mob lynching was an unprecedented event in modern Egyptian history.
Who is martyr Sheikh Hassan Shehata?
He was a prominent Shia cleric who had thousands of followers due to his moderate views and his denouncement of radical and extremist movements in Egypt.
He was one of the main religious figures advising the Egyptian army and was an Imam of one of the most important mosques in capital Cairo.
He was well known for telling people about the nature of extremist groups and radical thoughts which are common in Egypt due to powerful presence of radical Salafist groups.
His enlightenment was not welcomed in the ruling system.
In 2009 Sheikh Hassan spent some time in jail under the government of ousted Egyptian president Hosni Mubarak due to his speeches against radical movements harming Islam. 306 of his followers were also detained along with him.
This wasn’t the first time he was arrested; before that he was arrested in 1996 for what the then authorities called desecration of religions.
On June 23, 2013, Sheikh Hassan was brutally attacked at a gathering in the village of Zawiyet Abu Musalam by more than a thousand of Salafist extremists and along with 3 of his companions was harshly beaten to death.
In Egypt, the small Shia population is harassed by the authorities and treated with suspicion, being arrested - ostensibly for security reasons - but then being subjected to torrents of abuse by state security officers for their religious beliefs.
The Arab country has been witnessing a rise in hate crimes against Shias, which analysts believe is due to widespread anti-Shia propaganda by extremist Wahabis aimed at encouraging people to go fight alongside terrorists in Syria.
Critics warn that militant extremists are acting with dangerous impunity.
Murder of Sheikh Hassan
The brutal attack on Sunday (June 23, 2013) in the village of Zawiyet Abu Musalam, near the Pyramids of Giza, came as about 30 Shias were having a meal to mark a religious occasion. Hundreds of young men descended on them in the house.
In online videos of the killings, young men armed with metal and wooden clubs, swords and machetes, beat the Shias on the head and back, trapping them in the narrow entrance of the house.
The Shias beg for mercy as blood streams down their heads and soaks their robes. A crowd pressing around them triumphantly chanting and shouting. Some screamed "You sons of dogs!"
One video shows a young man dragging the motionless and bloodied body of one victim by a rope.
The videos appeared genuine and conformed with Associated Press reporting on the attack.
Afterward, the attackers congratulated each other, one witness, local activist Hazem Barakat, said in written and video account of the events he posted online.