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In his victory speech, he promised that poor Peruvians would share the country's mineral wealth and benefit from its impressive economic growth.
Ms Fujimori is the daughter of jailed ex-president Alberto Fujimori.
The two candidates are at opposite ends of the political spectrum - a fact that worried some Peruvians who said they would not vote for either of them.
It has been one of the tightest election races in Peru's recent history - and the bitterest, says the BBC's Dan Collyns in Lima.
But Ms Fujimori has said she will admit defeat if the official election results confirm her rival's narrow lead, and will not ask for a recount.
Reluctant voters This was a run-off vote after the first round on 10 April saw three centrist candidates defeated, but left neither Mr Humala nor Ms Fujimori with the 50% of votes needed to win outright.
If the Mr Humala is confirmed as the winner, he will succeed Alan Garcia, who could not stand for a second term.
Ollanta Humala, 48, comes from a left-wing tradition of greater state intervention. He staged a short-lived rebellion against Alberto Fujimori in 2000 and narrowly lost to Mr Garcia in the last presidential election in 2006.
He campaigned on a promise to increase the state's role in the economy and redistribute wealth to Peru's poor majority.
His critics fear he will embark on interventionist policies similar to those of President Hugo Chavez in Venezuela, although Mr Humala says he is more in sympathy with Brazil's moderate left-wing approach.
He has also denied allegations that he committed human rights abuses during the fight against Shining Path rebels in the 1990s when he was an army captain.
Keiko Fujimori, 36, appeals to Peruvians who still admire her father, president for a decade from 1990. He is now serving a 25-year jail sentence for corruption and organising death squads.
She has defended his record, saying by taming hyper-inflation and defeating Marxist Shining Path rebels, he laid the basis for Peru's current economic boom.
She supports free-market economic policies, advocates a tough approach to crime and promised to improve social programmes and infrastructure in poor areas.
Critics say her main aim by running for president was to secure a pardon for her father, a claim she denied.If the final result differs from the early count and she wins the election, she would become Peru's first woman president.
Voting is compulsory in Peru but surveys before the election suggested that around 10% of voters could abstain or spoil their ballots, Reuters news agency said.
Whoever finally triumphs will have the job of trying to pull back together a polarised nation, our correspondent says.
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