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 divise rule in July.
Yet the lower-than-expected turnout - Sisi himself had called for much more voters to come out - signalled that a wide segment of the population was apathetic or boycotted the election.
Morsi's Muslim Brotherhood, crushed by a massive crackdown following his overthrow and detention, had boycotted the vote.
Some journalists and government employees erupted in applause and began dancing as the final results were announced at a press conference Tuesday.