Naoot had been sentenced to three years in jail in January after she criticised in a Facebook post the slaughter of cattle and sheep for the Muslim holiday of Eid al-Adha.
She had left the country and returned last month as she appealed the ruling.
Naoot told AFP she intended to also appeal against Thursday's ruling, a suspended six-month sentence.
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"We will appeal it to have a final acquittal," she said.
"It is a clear signal that Egypt supports freedom of belief and expression," she added.
Earlier this month, President Abdel Fattah al-Sisi pardoned 82 prisoners, many of them activists, including an Islamic reform advocate sentenced to jail for criticising religious texts.
Author Ahmed Naji, sentenced to two years for sexually explicit passages in a novel, remains in prison.