Turnout in last week's election, hastily extended to three days amid fears of low turnout, was 47.45 per cent, said commission chief Anwar Rashad al-Asi.
Sisi's rival Hamdeen Sabbahi won just three per cent of the vote, excluding spoiled ballots.
Sisi's lopsided victory had been certain, with many lauding the retired field marshal as a hero for ending Morsi's divisive rule in July.
Yet the lower-than-expected turnout -- Sisi himself had urged more voters to come out -- signalled a wide segment of the population was apathetic or boycotted the election.
Some journalists and government employees erupted in applause and danced as the final results were announced at a press conference.
Police outside the press conference hall passed flowers to journalists as they left, and fruit juice cartons with a sticker reading: "Congratulations to Egypt."
Saudi Arabia's King Abdullah, who opposed Morsi's Muslim Brotherhood and backed his ouster, immediately called for a donors conference to help Egypt after the results were announced.
In Cairo's Tahrir Square, where protesters had battled police three years ago in an uprising to overthrow dictator Hosni Mubarak, several thousand Sisi supporters celebrated and set off fire works.
But her daughter, Hala Abu Fadl, 29, recalled the past violence in the iconic square, once synonomous with rebellion against Mubarak and the army, which took over between his overthrow and Morsi's election in June 2012.
"Celebrating here is difficult," she said, pointing to a mural depicting a slain protester, at the entrance of a street where activists clashed with police and soldiers in 2011.
"I voted for Sisi for stability, but I fear a crackdown on freedoms," she said.
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