The judge also reversed 492 death sentences out of 529 passed in March, commuting most to life in prison.
The cases and speed of the hearings have drawn widespread criticism from human rights groups and the UN.
The trials took just hours each and the the court prevented defence lawyers from presenting their case, according to Human Right Watch.
Correspondents said several female relatives waiting outside the courtroom fainted on hearing news of the verdict.
Last month, the UN human rights commissioner condemned the two trials and said they had breached international human rights law.
A spokesman for Navi Pillay said the "cursory mass trial" was "rife with procedural irregularities."
Authorities have cracked down harshly on Islamists since President Mohammed Morsi, who belongs to the Muslim Brotherhood, was removed by the military in July. Hundreds have been killed and thousands arrested.
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