Mohammed Badie, 71, was charged with killing at least nine people and inciting violence that injured 21 others in clashes near a mosque in Giza in July 23, 2013.
The court has also reduced the death sentence of seven other Brotherhood leaders.
In June, the Giza Criminal Court had sentenced Badie and 13 other high-profile Islamists to death in the case.
The ruling was sent to the Grand Mufti for review.
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The Mufti, then, asked the court to rethink about the ruling and decided to reject the death sentence against the leader of the banned Muslim Brotherhood group and 13 supporters on charges of murder and possession of firearms because there was no strong evidence.
The court has reduced the death sentence of Badie and seven other leaders, to life and confirmed death sentences to six other in absentia.
The Brotherhood was declared a terrorist group in December last year. It was accused of orchestrating a wave of violence to destabilise the country after the military overthrew Morsi in July 2013.
Since the ouster of Morsi, his group and loyalists have faced a state crackdown.
More than 1,000 people have been killed and 16,000 detained in a crackdown by the authorities on Morsi's supporters.
Badie had already received a confirmed death sentence in a separate case along with 182 supporters in a case which triggered outrage among rights groups.