Abdel Fattah al-Sisi, the general who toppled Egypt's first freely elected leader, took more than 90% of the vote in a presidential election, provisional results show.
However, 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.
Gen Sisi won 93.3% 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%, while 3.7% of votes were declared void.
Turnout was 44.4% of Egypt's 54 million voters, judicial sources said.
Gen Sisi's supporters waved Egyptian flags and sounded car horns in Cairo 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 Hosni Mubarak in 2011, and raised hopes of a democracy free of influence from the military.
Some Egyptians, exhausted after years of upheaval, have concluded that Gen Sisi is a strong figure who can bring calm, even though past leaders from the military mismanaged the country.
However, critics fear that Gen Sisi will become another autocrat who will preserve the army's interests and quash hopes of democracy and reform.
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.
Many Egyptians also feel Gen 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 in the next fiscal year.
Gen 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.
New York-based Human Rights Watch said the security crackdown after Mr 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 Whitson, TRW's Middle East and North Africa director, said.