Abdel Fattah al-Sisi, the retired field marshall who toppled Islamist president Mohamed Morsi last year, is expected to easily win, but his campaign had hoped for a large turnout as a decisive show of support.
After reports of a meagre turnout on Monday's first day of voting, Sisi's backers and sympathetic media harangued people to go and vote as Islamists had urged a boycott.
One television anchor, the ultra-nationalist Tawfiq Okasha, went as far as suggesting those who fail to vote should "be shot".
The decision to extend the voting into tomorrow was made to "give a chance to the largest possible number of voters to cast their ballots," said an electoral official.
The organisers of the vote said they extended the election because of a "heatwave that resulted in a crowding of voters during the evening hours".
Sisi's campaign also filed a complaint against the extension.
"We had hoped the commission would extend voting each day after 9:00 pm because it is very hot," Sisi's spokeswoman Mona el-Kouedi told AFP.
Morsi's Muslim Brotherhood, subjected to a police crackdown that has killed hundreds of its supporters, called for boycott and said it would not recognise the outcome.
So too have key activists behind the 2011 uprising that ousted long-time strongman Hosni Mubarak in 2011. They fear Sisi is an autocrat in the making.
Officials said the first day's turnout was about 16 million out of the country's 53 million eligible voters.
Interim prime minister Ibrahim Mahlab denied there was a low turnout, saying "participation is good".
"I don't want to be part of those responsible for all those people who died," Tarek Salim told AFP at a Cairo cafe.
Another abstainer, Diaa Hussein, complained there was no real choice, saying: "Sisi didn't leave a chance for anyone else to win".
Gamal Abdel Gawad, an analyst at the American University of Cairo, said the extension was unnecessary.
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