This is according to the Thursday provisional results, as he joined a long line of leaders drawn from the military.
But a lower-than-expected turnout figure raised questions about the credibility of a man idolised by his supporters as a hero who can deliver political and economic stability.
Sisi won 93.3 per cent of votes cast, judicial sources said, as counting neared its conclusion after three days of voting. His only rival, leftist politician Hamdeen Sabahi, gained 3 per cent while 3.7 per cent of votes were declared void.
Turnout was 44.4 per cent of Egypt's 54 million voters, judicial sources said, less than the 40 million votes, or 80 per cent of the electorate, that Sisi had called for last week and also less than the 52 per cent turnout Mursi won in 2012.
(READ MORE: Sisi on brink of presidency as Egyptians vote)
"We are now divided with the turnout," said Tarek Awad, 27 and unemployed, celebrating Sisi's victory in Tahrir on Thursday morning. "If about half of voters wanted Sisi, the other half don't want him. What about them?"
The stock market .EGX30, which fell 2.3 per cent on Wednesday as some players said the turnout was a disappointment, was down a further 0.9 per cent by late morning on Thursday. On the black market, the Egyptian pound weakened slightly.
Mohamed El Sewedy, chairman of the Federation of Egyptian Industries, said, however: "The business community is very happy about the results. My friends and I have a lot of hope.”
Others saw the stability offered by Sisi as important.
"Everybody just wants some form of stability against which you can decide what to invest. When there's stability it makes risk assessment much easier," said Angus Blair, chairman of business and economic forecasting think-tank Signet.
Most Egyptian newspapers celebrated the result, with state-run Al-Akhbar calling it "a day of hope for all Egyptians".
Fireworks erupted in Cairo to celebrate Sisi's victory late on Wednesday. His supporters waved Egyptian flags and sounded car horns as celebrations lasted through the early hours of the morning.
About 1,000 people gathered in Tahrir Square, the symbolic heart of the popular uprising that toppled Mubarak in 2011 and raised hopes of a democracy free of influence from the military.
As Egyptians travelled to work, there were only a handful of Sisi supporters left in Tahrir.
(READ MORE: Egyptians slow to vote despite efforts to boost turnout)
Sisi, who ousted Mursi last year after mass protests against his rule, is seen by supporters as a strong figure who can end the turmoil that has convulsed Egypt for three years since the revolution that ousted Hosni Mubarak after 30 years in power.
Critics fear Sisi will become another autocrat who will preserve the army's interests and quash hopes of democracy and reform.
Sisi enjoys the backing of the powerful armed forces and the Interior Ministry, as well many politicians and former Mubarak officials now making a comeback.
"This is the best possible result. He is from the army, so he knows Egypt," Yeshiva Hassan, a vendor selling radios on a downtown Cairo street, said.
But the former military intelligence chief may not have the popular mandate to take the tough measures needed to restore healthy economic growth, ease poverty and unemployment, and end costly energy subsidies in the most populous Arab nation.
In a country polarised since the revolt against Mubarak, many Egyptians said voters had stayed at home due to political apathy, opposition to another military man becoming president, discontent at suppression of freedoms among liberal youth, and calls for a boycott by Islamists.
Horsham Moans, Sabahi's campaign manager, questioned the legitimacy of the vote, saying there had been violations.
"Until yesterday turnout was much lower than what was announced today. Did the percentage suddenly reach 46 per cent?"
An editorial in state-run Al-Ah ram newspaper called for "a serious and real pause" to review the past three days' events.
"The behaviour and style of some almost corrupted the image and contributed to the impression that what happened did not follow the conditions of a proper democratic process or fair competition", it said.
New York-based Human Rights Watch (HR) said the security crackdown after Mursi's ouster had created a repressive environment that undermined the fairness of the election.
“The mass arrests of thousands of political dissidents, whether Islamist or secular, has all but shut down the political arena and stripped these elections of real meaning,” Sarah Leah Whit son, TRW's Middle East and North Africa director, said.
Some Egyptians, exhausted after years of upheaval, have concluded that Sisi is a strong figure who can bring calm, even though past leaders from the military mismanaged the country.
Despite an official campaign to bring out more voters, Egyptians, many opposed to Sisi, gave various reasons for their lack of enthusiasm.
Young secular activists, including those who backed Mursi's ouster, had become disillusioned with Sisi after many were rounded up in the crackdown that also restricted protests.
Since he gave a series of television interviews, many Egyptians feel Sisi has not spelled out a clear vision of how he would tackle Egypt's challenges, instead making a general call for people to work hard and be patient.
He has presented vague plans to remedy the economy, suffering from corruption, high unemployment, and a widening budget deficit aggravated by fuel subsidies that could cost nearly 19 billion dollars in the next fiscal year.
Sisi also faces the formidable challenge of crushing an Islamist armed insurgency and eliminating any threat from the Brotherhood, which, as the country's best-organised political force, had won every national vote held after Mubarak's fall.
The Muslim Brotherhood, a movement loyal to Mursi and outlawed as a terrorist group by the military, has rejected the election, describing it as an extension of the army takeover.
The Brotherhood, believed to have about one million members in a country of 85 million, has been devastated by one of the toughest crackdowns in its history. Its top leaders, including Mursi, are on trial and could face the death penalty. The movement seemed inspired by the low turnout in this week's poll.
"Sisi and those with him have to admit that Egypt is against them and the Dr. Mohamed Mursi is their president and the president of all Egyptians,” an Islamist alliance that includes the Brotherhood said in a statement.
The United States, Egypt's ally in the West, has yet to comment on Sisi's victory.