Presidency spokesman Alaa Youssef said the two Al-Jazeera colleagues Mohamed Fahmy and Baher Mohamed were among the pardoned group of 100 prisoners.
Following the announcement, Fahmy and Mohamed were dropped off by officials in Maadi near here.
Canadian Al-Jazeera journalist 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, whose initial arrest was in December 2013, had a dual Egyptian-Canadian nationality but gave up his Egyptian nationality in an effort to get deported.
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.
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.
