The judgment by the court of cassation against the sentence, handed out in 2016, cannot be appealed.
Badie, 74, was convicted for his role in violence that broke out in the Suez Canal city of Ismailia days after the army, led by then Gen. Abdel Fattah El-Sisi, toppled President Mohamed Mursi following mass demonstrations against him.
Sissi was elected president the following year.
In the same case, the court on Wednesday also upheld life sentences against seven other people and handed 10-year sentences to 39 and three-year sentences to 19 others.
They were charged with killing three people and attempting to kill 16 others, thuggery, and vandalising public property among other offenses, related to the clashes in Ismailia in July 2013.
Authorities outlawed the Brotherhood after Mursi was ousted, and arrested thousands of its supporters. They also dissolved its Freedom and Justice Party, which Mursi led.
Badie has also been sentenced to life in eight other cases, only one of which has been confirmed. Two were canceled, two are pending appeal and three the subject of retrials.