With almost 15 per cent of polling stations accounted for, the retired field marshal led with about 93 per cent of votes cast over the three-day election, trouncing his sole rival Hamdeen Sabbahi.
The outcome had never been in doubt, with Sisi riding on a wave of support for a potential strongman who can restore stability after several years of tumult.
But the army-installed government and Sisi were eyeing a large turn out as an endorsement of Morsi's overthrow in July and a crackdown on his supporters.
Voting was meant to end on Tuesday, but was extended for a day in a last minute decision that sparked protests from Sabbahi, a leftist politician who came in third in the 2012 election Morsi won.
Sabbahi received 133,548 votes (2.95 per cent) to Sisi's 4,215,699 (93.3 per cent) in the latest polls, according to the official Nile Television.
The station reported that 166,738 voters (3.7 per cent) spoiled their ballots in the 2,000 out of 13,899 polling stations that released their tallies.
Turn out figures were not immediately available.
The move to extend polling for a day fuelled criticism of an election already marred by a deadly crackdown on Morsi's Muslim Brotherhood movement.
An electoral official said on Tuesday that turnout was about 37 per cent, well below the 52 per cent of voters who cast their ballots in the 2012 election Morsi won.
The lower turnout came despite a personal appeal from retired field marshal Sisi, who had been seeking vindication for his July overthrow of Morsi, Egypt's only freely elected president, after a single turbulent year in power.
Sisi had urged "40, 45 (million) or even more" of Egypt's 53 million eligible voters to turn out to give credibility to an election boycotted by Morsi's Muslim Brotherhood and secular opposition groups.
After reports of meagre numbers at polling stations on the first day of voting Monday, Sisi's backers in the state-run media appealed to people to go out and vote.
On Wednesday, several Cairo polling stations were nearly deserted.
"They didn't get enough votes, so they extended polling into a third day," complained filmmaker Mohamed Ali Hagar, who said he would stay away regardless.
"The state is searching for votes," said a front-page headline of Al-Masry Al-Youm, a newspaper that usually backs Sisi.
The extension of polling casts doubt on the vote's credibility, experts said.
It "raises more questions about the independence of the electoral commission, the impartiality of the government, and the integrity of Egypt's electoral process," said Democracy International, a US-based observer mission.
That echoes criticism from Sabbahi, who said on Tuesday that the extension raises "questions... about the integrity of the process".
Sisi's campaign team too filed a complaint against the move, suggesting an extra day of polling might be a burden on voters.
The Muslim Brotherhood, which had championed a boycott of the election, hailed the low turnout.
"The great Egyptian people have given a new slap to the military coup's roadmap and... written the death certificate of the military coup," said its political arm, the Freedom and Justice Party.
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