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Sisi's only rival, leftist Hamdeen Sabbahi, won less than four percent, according to the preliminary results.
The longtime opposition figure conceded defeat Thursday but cast doubt on the estimated turnout of 47 percent after calls for a high participation rate as a sign of legitimacy.
Ahead of the final results due within a week, hundreds of Sisi supporters took to the streets on Wednesday night to celebrate, waving Egyptian flags, setting off fireworks and honking car horns.
"It's a victory for stability," said Tahra Khaled, among the crowd in Cairo's Tahrir Square, nerve centre of the mass protests that forced autocratic president Hosni Mubarak to step down in 2011.
Sisi, who retired from the army to run for office, becomes Egypt's fifth president from the military, reasserting the institution's grip on politics in the Arab world's most populous nation.
The military has always formed the backbone of political life in Egypt and the institution has provided its leaders ever since army officers toppled the monarchy in 1952.
The only exception was Morsi, elected a year after the fall of former air force commander Mubarak.
"Few would have imagined that... three years after Mubarak's toppling, a field marshall, a new pharaoh, would be elected again with 96 percent, without even unveiling a programme and without campaigning," said analyst Karim Bitar.
Sisi rode on a wave of support for a potential new strongman who can restore stability and revive the economy after three years of turmoil.
But his opponents say that since he ousted Morsi last July, Egypt returned to autocracy.
A state crackdown targeting Morsi supporters has left at least 1,400 people dead in street clashes and seen more than 15,000 others jailed.
Dozens of young activists have also been jailed for violating a law banning all but police-authorised protests.
A European Union team that observed the election said Thursday the vote was conducted "in line with the law," but regretted the lack of participation of some "stakeholders," a likely reference to Morsi's banned Muslim Brotherhood and youth dissident groups.
- Opposition hails boycott -
Amid the crackdown on dissent condemned by rights groups and Western governments, the military-installed authorities had aimed for a high turnout as a sign of legitimacy.
Private and state-run media pressed Egyptians to go out and vote, and the election was extended for a third day in a last-minute decision which sparked protests.
Sisi had called for at least 40 million of Egypt's almost 54 million electorate to go to the polling stations.
Although it could edge higher, authorities put actual turnout at about 25 million, or 47 percent, down from 52 percent when Morsi was elected in 2012.
"Ultimately, we have no real way to verify (government) turnout numbers" or Sisi's victory margin, Shadi Hamid of the Brookings Institution's Saban Center wrote on Twitter.
He pointed to the absence of "parallel counts and not enough (international) monitors."
Egyptian authorities are touting the election as a milestone on the road to democracy following Morsi's ouster, but Human Rights Watch says the crackdown "stripped these elections of real meaning".
"The intense crackdown on dissent over the last 10 months has created a repressive environment that severely undermines the fairness of the elections," it said.
In Washington, State Department spokeswoman Jen Psaki said the United States was waiting for official results, but that "we remain concerned... about the continued restrictive political environment leading up to the elections and its implications for inclusivity and stability in Egypt, including politicised arrests and limits on freedom of the press.
"Democracy is more than elections, and we will continue to press for progress on all of those areas."
The Muslim Brotherhood hailed what it sees as a successful boycott.
"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.
All of the movement's main leaders are now in jail or exile, and Morsi himself is being tried on charges that could carry the death penalty.
Prominent activists behind the uprising that ousted Mubarak three years ago had also called for a boycott, charging that Sisi is an even worse autocrat in the making.
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The longtime opposition figure conceded defeat Thursday but cast doubt on the estimated turnout of 47 percent after calls for a high participation rate as a sign of legitimacy.
Ahead of the final results due within a week, hundreds of Sisi supporters took to the streets on Wednesday night to celebrate, waving Egyptian flags, setting off fireworks and honking car horns.
"It's a victory for stability," said Tahra Khaled, among the crowd in Cairo's Tahrir Square, nerve centre of the mass protests that forced autocratic president Hosni Mubarak to step down in 2011.
Sisi, who retired from the army to run for office, becomes Egypt's fifth president from the military, reasserting the institution's grip on politics in the Arab world's most populous nation.
The military has always formed the backbone of political life in Egypt and the institution has provided its leaders ever since army officers toppled the monarchy in 1952.
The only exception was Morsi, elected a year after the fall of former air force commander Mubarak.
"Few would have imagined that... three years after Mubarak's toppling, a field marshall, a new pharaoh, would be elected again with 96 percent, without even unveiling a programme and without campaigning," said analyst Karim Bitar.
Sisi rode on a wave of support for a potential new strongman who can restore stability and revive the economy after three years of turmoil.
But his opponents say that since he ousted Morsi last July, Egypt returned to autocracy.
A state crackdown targeting Morsi supporters has left at least 1,400 people dead in street clashes and seen more than 15,000 others jailed.
Dozens of young activists have also been jailed for violating a law banning all but police-authorised protests.
A European Union team that observed the election said Thursday the vote was conducted "in line with the law," but regretted the lack of participation of some "stakeholders," a likely reference to Morsi's banned Muslim Brotherhood and youth dissident groups.
- Opposition hails boycott -
Amid the crackdown on dissent condemned by rights groups and Western governments, the military-installed authorities had aimed for a high turnout as a sign of legitimacy.
Private and state-run media pressed Egyptians to go out and vote, and the election was extended for a third day in a last-minute decision which sparked protests.
Sisi had called for at least 40 million of Egypt's almost 54 million electorate to go to the polling stations.
Although it could edge higher, authorities put actual turnout at about 25 million, or 47 percent, down from 52 percent when Morsi was elected in 2012.
"Ultimately, we have no real way to verify (government) turnout numbers" or Sisi's victory margin, Shadi Hamid of the Brookings Institution's Saban Center wrote on Twitter.
He pointed to the absence of "parallel counts and not enough (international) monitors."
Egyptian authorities are touting the election as a milestone on the road to democracy following Morsi's ouster, but Human Rights Watch says the crackdown "stripped these elections of real meaning".
"The intense crackdown on dissent over the last 10 months has created a repressive environment that severely undermines the fairness of the elections," it said.
In Washington, State Department spokeswoman Jen Psaki said the United States was waiting for official results, but that "we remain concerned... about the continued restrictive political environment leading up to the elections and its implications for inclusivity and stability in Egypt, including politicised arrests and limits on freedom of the press.
"Democracy is more than elections, and we will continue to press for progress on all of those areas."
The Muslim Brotherhood hailed what it sees as a successful boycott.
"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.
All of the movement's main leaders are now in jail or exile, and Morsi himself is being tried on charges that could carry the death penalty.
Prominent activists behind the uprising that ousted Mubarak three years ago had also called for a boycott, charging that Sisi is an even worse autocrat in the making.
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