Al-Sisi is hoping for a large turnout to send a message to the West that his removal almost a year ago of the Islamist Mohamed Morsi - Egypt's first freely elected leader - was not a coup but a popular revolution like the 2011 uprising that ended autocrat Hosni Mubarak's rule.
Election monitoring groups said the turnout on Monday was moderate and in towns where Islamists dominate, often thin or non-existent.
This apparently prompted the government to declare Tuesday a public holiday to allow millions of government employees time to go and cast ballots, and extended voting hours by one hour.
Al-Sisi is expected to emerge from a second and final day of voting on Tuesday as Egypt's next president, with supporters seeing him as the man who can pull the Arab world's most populous nation back from the brink.
The vote - with initial results expected hours after polls close at 9 p.m. (1800 GMT) on Tuesday evening - means Egypt will likely revert to rule by men from the military after Sisi toppled the country's first freely elected leader, Mohamed Morsi of the Muslim Brotherhood.
Former army chief Sisi faces only one challenger: The leftist politician Hamdeen Sabahi. Other candidates who contested the 2012 election won by Morsi did not run, saying the climate was not conducive to democracy.
Despite calls for a big turnout by Sisi and media loyal to the army, the turnout on Monday appeared lower than in previous elections. With Sisi seemingly assured of victory, he needs a good turnout to shore up his legitimacy.
Lines at 20 Cairo polling stations visited by Reuters consistently over the past three years appeared shorter than in previous elections. The interior minister said turnout was good.
As polls were about to close after the first day of voting on Monday, there was no sign of a late rush. The supervisor of a polling station in a working-class district of Cairo told Reuters fewer than 30 percent of registered voters had shown up.
Earlier on Monday, it was hard to find anyone who planned to vote for Sabahi in lines of voters where young Egyptians - the generation that drove the "Arab Spring" uprising - were conspicuous by their absence.
Many of Sisi's supporters said they voted for stability rather than Western-style democracy, which they felt had brought chaos and hardship into their lives.
"The Egyptian people and democracy, it doesn't work like it does in Europe," said Ahlam Ali Mohamed, a 47-year-old housewife in Alexandria, who voted for Sisi. "I voted today because I want to feel safe."
Although he enjoys the adulation of many Egyptians, Sisi, 59, faces serious challenges including an economy in crisis and a campaign of Islamist violence that has spiralled since he overthrew Morsi.
To the Islamists, he is the author of a coup followed by a bloody crackdown that killed hundreds of Morsi supporters and landed thousands more in jail. Secular dissidents who led the Jan. 25 uprising against Mubarak have also been imprisoned.
Human Rights Watch estimates the number of political dissidents and Islamists in detention at more than 20,000.
At the same time, several hundred members of the security forces have been killed in a campaign of violence by radical Islamists since last July. The last year has been the bloodiest period of internal strife in Egypt's modern history.
The Brotherhood and its allies, which had declared it "the election of the presidency of blood", issued a statement saying their call for a boycott had been widely observed. The group has been declared a terrorist organization by the state, which accuses it of turning to violence - a charge it denies.
Sisi won 95 percent of votes cast in advance by Egyptians abroad, but an opinion poll by the Washington-based Pew Research Center suggests a more mixed picture, with Sisi viewed favourably by 54 percent and unfavourably by 45 percent.
As Sisi voted in Cairo on Monday, he waved to supporters, who shouted "President, President!"
"Today Egyptians are going to write their history," said Sisi.
It is the second time Egyptians are electing a president in two years. And it is the seventh vote or referendum since 2011.
Once president, Sisi will nonetheless have to meet the high expectations of those who backed him so enthusiastically in the hope that he can tackle poverty, unemployment and other social problems.
He will also be expected to address the corruption, cronyism and inequality between rich and poor that caused the 2011 revolution that overthrew Mubarak.
Sabahi's campaign team complained of violations including the arrest of one of its members.
Since the army overthrew the king in 1952, Egypt has been ruled by a succession of military men - Gamal Abdel Nasser, Anwar Sadat and Mubarak. That pattern was briefly interrupted by Morsi's divisive year in office, during which important institutions of state resisted his authority.
The 2012 election won by Morsi was a tightly contested race fought by around a dozen candidates.
Sisi, quietly spoken former head of military intelligence, has in turn mobilised religion against the Islamists, presenting himself as a God-fearing defender of Islam.
The Associated Press and Reuters contributed to this report