With more than half of the ballots counted, al-Sissi had won 10.35 million votes while his lone opposition-left-wing opponent, Hamdeen Sabahi, won just 333,566 votes.
Al-Sissi supporters have begun celebrations in Cairo, with several thousands gathered at the central Tahrir square.
Eyewitness reports say there were smaller crowds in two other Cairo districts and in towns across much of the country.
Al-Sissi is Egypt’s president elect.
While his victory was never in doubt, his campaign had hoped for a strong turnout to confer legitimacy on his candidacy and presidency.
Al-Sissi ousted Egypt’s freely elected president Mohamed Morsi and led a forceful operation against his Muslim Brotherhood and supporters.
Upon running the Muslim Brotherhood out of political significance in Egypt, Al-Sissi, who insisted his actions were backed by most Egyptians, retired from the military and ran for president.
However, the nationwide turnout for the elections did not suggest a positive perception of the events since al-Sissi ousted Morsi.
Al-Sissi wanted more than 40 million voters- more than 80 percent of Egyptians to cast ballots, so the world can perceive his efforts in a positive light.
However, only around 44 percent of Egyptians came out to vote even after voting was extended for third day Wednesday.
Many in Egypt have been disenchanted by events since the revolution that brought down Hosni Mubarak.
“People are lazy, depressed or frustrated. They knew what the result will be even before the vote,” AP quoted Amani Fikry, a manager in a privately-owned company.
“They are exhausted from three years of constant troubles.”
Some fear that al-Sissi has no concrete plans for Egypt’s problems and that Al-Sissi will return Egypt to the autocratic ways of Mubarak.
Egypt’s interim government and local media built up Al-Sissi as a warrior against terrorism and the only person able to tackle Egypt’s economic problems, high unemployment, inflation and instability.
Understand Africa's tomorrow... today
We believe that Africa is poorly represented, and badly under-estimated. Beyond the vast opportunity manifest in African markets, we highlight people who make a difference; leaders turning the tide, youth driving change, and an indefatigable business community. That is what we believe will change the continent, and that is what we report on. With hard-hitting investigations, innovative analysis and deep dives into countries and sectors, The Africa Report delivers the insight you need.View subscription options