While President Goodluck Jonathan was the favourite going in to the race in Africa's most populous nation, turnout appeared especially strong in the north, the stronghold of his main opponent, ex-military ruler Muhammadu Buhari.
Early results from various districts published by local newspapers showed Buhari performing well in the north and Jonathan strong in the south, raising the possibility of a runoff between the two.
Given the size of Nigeria -- a country of some 150 million people -- it remained too early to draw any firm conclusions on Saturday's vote.
The electoral commission has said it intends to release full results within 48 hours after the end of voting in Africa's largest oil producer.
"There's good news in this Nigerian presidential election: we're counting actual votes and people are interested in the count," said Chidi Odinkalu of the Open Society Justice Initiative NGO.
"And quite bad news: the country is badly divided, north vs. south."
It is a scenario many analysts had hoped to avoid in a country as fractious as Nigeria, a nation of some 250 ethnic groups and roughly divided in half between Christians and Muslims.
In the months leading up to the polls, the ruling Peoples Democratic Party sought to heal internal rifts over whether it should abandon Jonathan, a southern Christian, in favour of a candidate from the north.
Jonathan, the first president from the oil-producing Niger Delta region, won out in the end, but bitterness remained. Many in the north saw Buhari as their chance to return power to their economically marginalised region.
A crowd of hundreds loudly greeted Buhari when he arrived at his polling place in his hometown of Daura on the edge of the Sahara, with some climbing on a rooftop to see him and yelling "Allahu Akbar!"
After voting, Buhari alleged there had been reports of electoral fraud.
Several newspapers on Sunday highlighted the regional divisions early results were showing.
ThisDay newspaper reported that the early results "were reflective of the sectional divide between the north and south, with voters from both sides casting their votes along regional and religious lines."
A candidate must do more than carry the most votes to be declared the winner, with the constitutional spelling out that one-quarter of the ballots in at least two-thirds of the states must also be captured.
If that is not achieved, a runoff is to be held, which would throw Nigeria into a scenario it has not experienced since the end of military rule in 1999. The ruling PDP has handily won every presidential vote since then.
The election was a bid by Nigeria to hold its cleanest polls for head of state in nearly two decades after a series of violent and deeply flawed ballots.
A number of observers gave the poll an initial thumbs up, with voting stations generally opening on time and balloting calm in most of the country.
However, there were a number of violent incidents. Three explosions hit the north -- one on Friday night and two on Saturday -- with police saying eight were wounded from one of the blasts.