Mohammed Fahmy, a Canadian, and Baher Mohamed, an Egyptian, were among 100 prisoners whose release was ordered.
State media said a third person from the case was also pardoned. It is not clear if this is the Australian Peter Greste, who was deported in February.
They were sentenced to three years in prison last month after a retrial.
Prosecutors accused them of collaborating with the outlawed Muslim Brotherhood after the overthrow of President Mohammed Morsi by the military in 2013.
The journalists denied the allegation and said they were simply reporting the news. Legal experts said the charges were unfounded and politically motivated.