Mohamed Badie made the comments about Monday's sentencing from the caged dock at another trial in which he, Morsi and others are accused of plotting attacks and prison breaks.
Since Morsi's overthrow by the military in July, the army-installed government has conducted an extensive crackdown that has left at least 1,400 people dead and thousands in prison.
The mass death sentences, the second in as many months, sparked global outrage, with the United States urging the government to reverse the judgement.
"The coup will end," he said.
The court later sentenced another defendant, firebrand preacher Safwat Hegazy, to one year in prison for contempt after he called out to the judge using his first name.
Courts have sentenced several Islamist defendants in other trials on similar grounds in the past few months.
Morsi, who often tries to interrupt court proceedings with speeches, added: "This farce will end."
Morsi faces three trials, all of which can lead to the death sentence. Much of the leadership of his Brotherhood movement has been arrested and put on trial.
The same judge had sentenced 529 people to death on similar charges in March, but later commuted the sentences of most to life in prison.
Justice Minister Nayer Abdel-Moneim Othman defended the judiciary at a news conference today, saying it was "independent".
But he stressed that Monday's sentencing was preliminary and could be appealed.
"Why is there an appeal process? Because the judge is a human. He can make a mistake," he said.
The judge, Said Youssef Sabry, has a built a reputation for tough sentences. He is scheduled to confirm or commute the sentences on June 21.
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