The country's electoral commission said some 300 of the 150,000 polling stations would be open from 0700 GMT to accredit voters after handheld devices to read biometric identity cards failed.
Nigeria's ruling Peoples Democratic Party (PDP) called the situation a "huge national embarrassment" after President Goodluck Jonathan was affected by the malfunction as he tried to register yesterday.
The ruling party said repeatedly throughout the campaign that the technology should not be used as it was untested and there were questions about officials' ability to use it.
With the election closely fought, both parties looked set to keep the issue alive. Voters will be accredited throughout the morning either with the devices or if they fail again, by hand.
The chairman of the Independent National Electoral Commission (INEC), Attahiru Jega, sought to downplay the malfunctions, saying it was limited to "only about 450" card readers.
But he told the private Channels television that provision for a second day of voting was granted because it was a democratic right for citizens.
Yesterday, many voters camped overnight or arrived early at polling stations to have their credentials checked before returning to vote in the afternoon and long into the night.
The final voters cast their ballot in the dark and the count was started at many polling stations by flashlight, with Nigeria hit by regular, daily power cuts.
Government spokesman Mike Omeri claimed it was a "record high voter turnout", without giving figures, adding that it was a "triumph of Nigerian democracy" despite the polling problems.
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