The 59-year-old former army chief won 96.2 per cent of about 21 million votes cast, state TV reported early today, with the ballots from 312 of 352 counting stations tallied.
His only rival, leftist politician Hamdeen Sabahi, gained 3.8 per cent while 4.2 per cent of votes were declared void.
Voter turnout was low at 44.4 per cent despite the government extending the election for a third day. The turnout was lower than the election that brought Morsi to power in 2012.
Since Morsi's overthrow, more than 1,400 people have been killed and thousands of members of Muslim Brotherhood detained by authorities, who have designated the Islamist movement a terrorist group.
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Sisi's supporters started celebrations when results began to emerge. They waved Egyptian flags, sounded car horns on the crowded streets of the capital and and set off the fireworks.
Al-Jazeera reported that about 1,000 people assembled at Tahrir Square, the symbolic heart of a popular uprising that toppled longtime dictator Hosni Mubarak in 2011, and raised hopes of a democracy free of influence from the military.
He is popular among Egyptians who supported the army's decision to remove Morsi from power.
His supporters see him as the kind of strongman needed to end the turmoil dogging Egypt since a popular uprising ended Mubarak's three decades of one-man rule in 2011.
But Sisi is reviled by the Islamist opposition, which sees him as the mastermind of a coup against an elected leader and the author of a fierce crackdown on dissent.