Presidency spokesman Alaa Youssef said the two Al-Jazeera colleagues Mohamed Fahmy and Baher Mohamed were among the pardoned group.
Mohamed did not appear to be on the list when it was first published, nor did Australian Peter Greste, who was deported in February.
Fahmy was sentenced to three years in prison last month. He was jailed on charges, including joining an outlawed group -- the Muslim Brotherhood -- obstructing governmental institutions and law, attacking the personal liberty of citizens and harming national unity and social peace.
Mohamed, who was charged in the same case, was also pardoned. He was jailed for three years on charges of aiding the Brotherhood and handed an extra three-year term for his alleged possession of a spent bullet.
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Their detention and trial sparked global criticism who has said he wished the journalists had been deported from the outset rather than put on trial.
Their arrest in 2013 came at a time of deadly crackdown on the Muslim Brotherhood following Islamist leader Mohamed Morsi's overthrow by the military.
Egypt's controversial protest law was passed in November 2013 and states that protesters have to give the authorities a three-day notice before protesting.
Violators face hefty fines and prison sentences. The President traditionally pardoned groups of prisoners on national and religious holidays.
"This newest batch of youth pardoning comes as part of an initiative, launched by the president in December 2013, to release groups of youths," Youssef said.