The verdict of seven years in prison against the journalists brought a landslide of international condemnation.
Rights groups described their 5-month trial as a sham, with no evidence presented to back the terrorism related charges against them, saying the three were being punished simply for their reporting on protests by backers of ousted Islamist President Mohammed Morsi.
The White House said the ruling "flouts the most basic standards of media freedom" and was a "blow to democratic progress."
Australia and other governments have also urged el-Sissi to do so for the three journalists, whose families have said they will appeal. Appeals could take months, and the three are likely to remain in prison during the process.
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In a televised address to graduating military cadets, el-Sissi said, "We will not interfere in court verdicts" -- repeating the phrase twice in his speech to drive home the point.
He said he spoke to the justice minister yesterday and "told him one word: We will not interfere in judicial matters because the Egyptian judiciary is an independent and exalted judiciary."
Under the constitution, the president has the power to issue a pardon or commute the sentences.
The journalists' arrest last December was part of the broad crackdown against Islamists and the Muslim Brotherhood after el-Sissi -- in his former post of army chief -- removed Morsi last summer.
The journalists' trial was further politicised by the Egyptian government's deep enmity with the Gulf nation Qatar, which was a strong ally of Morsi's Brotherhood and owns the Al-Jazeera network.