Australia's Peter Greste, Canadian Mohamed Fahmy and Egyptian Baher Mohamed, all journalists with the Qatari-owned channel, were originally sentenced to up to 10 years in prison for allegedly aiding the blacklisted Muslim Brotherhood.
However, an appeals court overturned that verdict in January and ordered a retrial.
Greste was deported on February 1 under a presidential decree that allows the authorities to expel foreigners charged in Egypt and see them instead face trial in their home countries.
In a bid to secure his own deportation, Fahmy has renounced his Egyptian nationality and is awaiting a return to Canada.
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However, the third journalist, producer Mohamed, remains in jail as he has only Egyptian nationality.
The three employees of the Qatari-owned Al-Jazeera English broadcaster were arrested in December 2013 and tried for allegedly supporting the Brotherhood.
In June last year Greste and Fahmy were jailed for seven years, while Mohamed was sentenced to 10 years in prison before a retrial was ordered.
The journalists' initial trial came against the backdrop of a cold war between Egypt and Qatar, which supported the Islamist movement of president Mohamed Morsi, whom then army chief and now President Abdel Fattah al-Sisi deposed in July 2013.