Nigeria's ruling party candidate and former Lagos governor Bola Tinubu was ahead in the vote count from Saturday's presidential election, a Reuters tally of provisional results in 12 of 36 states showed.
But outsider Peter Obi of the smaller Labour Party defeated his ruling party challenger to win Nigeria's commercial hub of Lagos in a major upset in the poll which was marred by delays and complaints of irregularities.
The tally of provisional electoral commission results showed Tinubu, of the ruling All Progressives Congress (APC) party, ahead with about 3.7 million votes, against Atiku Abubakar of the main opposition People's Democratic Party (PDP) with about 2.5 million.
Obi was in third place with about 1.3 million.
Around two thirds of states in Africa's most populous country have yet to declare.
But the win in Lagos state - with 582,454 votes against 572,606 for Tinubu - was a major boost for Obi, whose run challenged candidates from two long-established movements that have alternated in power since the end of army rule in 1999.
Obi's campaign grabbed headlines with its use of social media and its focus on young people and urban voters fed up with widespread corruption and insecurity.
To become president, a candidate needs to get more votes than any other candidate and also garner a quarter of the votes in at least 24 states.
Electoral observers and all three major parties pointed out irregularities, many of them the result of technical glitches. The election was highly dependent on communications technology in a country with often poor internet coverage.
Obi's Labour Party and PDP campaign spokesperson Dino Melaye castigated the electoral body for the failure, in many places, to upload results directly from each polling unit to its website, as it had promised to do to guarantee transparency, a criticism echoed by Commonwealth observer mission chief Thabo Mbeki.
The European Union observer mission said: "INEC's lack of efficient planning in critical stages and effective public communication reduced trust in the process, including on election day."
By 1430 GMT on Monday, INEC had uploaded results from just 59,496 polling units out of a total of 178,846, its website showed.
"We take full responsibility for the problems and regret the distress that they have caused the candidates, political parties and the electorate," the commission said.
There have been reports of violence and intimidation, though not at the scale of previous elections.
In northern Kano state, police said a group had attacked a campaign office for a smaller opposition party and set the building on fire, killing two people.
Police said they had killed one of the attackers and arrested four suspects.
(Additional reporting by Hamza Ibrahim in Kano, Ahmed Kingimi in Maiduguri, Anamesere Igboeroteonwu in Onitsha, Tim Cocks in Lagos, Felix Onuah and Camillus Eboh in Abuja; Writing by Tim Cocks; Editing by Andrew Heavens and Nick Macfie)
