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.
‘Long nightmare ends’
A statement from President Sisi’s office issued on Wednesday Fahmy and Mohamed were named on a decree pardoning 100 young people “who had received final court sentences, having been convicted on the grounds of violating the anti-protest law and assaulting police forces”.
“Other prisoners were pardoned due to their health conditions and on humanitarian grounds,” it added.
Also named were the prominent activists Yara Sallam and Sanaa Seif, who were jailed in 2014 for taking part in an “illegal protest”.
His brother, Adel, told the BBC by telephone from Kuwait: “It’s such a relief to have this long nightmare end.
“We’re just so happy that this is all corrected and the truth has prevailed. He was always innocent.”
Al Jazeera in a report on its website that it “continues to demand all charges and sentences against its journalists are dropped”, noting that Greste and six other employees had been convicted in absentia.
The pardons were issued by Mr Sisi ahead of the Islamic festival of Eid al-Adha and a day before he travels to New York to address the UN General Assembly.
He had said he would be willing to pardon the Al Jazeera journalists once the judicial process had ended.
Fahmy, who renounced his Egyptian citizenship to qualify for deportation in February, was expected to leave for Canada following his release.
The case against the journalists began in December 2013, when they were arrested at a hotel used by Al Jazeera English to report from Cairo after its bureau was raided by police.
The journalists were initially convicted in June 2014 after a trial that was widely condemned. Greste and Fahmy were sentenced to seven years in prison, while Mohamed was given a 10-year sentence after also being found guilty of possessing a spent bullet casing.
In January, Egypt’s Court of Cassation ordered a retrial after ruling that the original court had been “hasty in pronouncing its verdict”.
Their convictions at retrial on 29 August were described as an “outrage” and an embarrassment for President Sisi by Amal Clooney, one of Fahmy’s lawyers.