"We have won the presidential elections," Humala told journalists, after official results of almost 80 percent showed Humala with 50.5 percent against 49.5 percent for Fujimori.
"We'll continue to follow the count until the confirmation of official results, but I'm going to share with the people ... the joy of our victory," Humala said at his Lima headquarters.
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Votes from rural areas favorable to Humala over right-wing rival Keiko Fujimori were yet to be counted more than seven hours after the close of polling.
Earlier, quick counts by three polling institutes showed 48-year-old Humala had a lead of between two and 4.4 points over 36-year-old Fujimori.
Humala campaigned on promises of sharing out Peru's rich mineral wealth after a decade of record growth and sought to play down former ties to anti-liberal Venezuelan President Hugo Chavez.
On Sunday, he promised to "continue with economic growth, and this growth will be the great motor of social development in the country."
Around 20 million people were eligible to vote, from the Amazon forest to the Pacific coast and remote areas of the Andes.
Keiko Fujimori campaigned in the shadow of her father, Alberto Fujimori, who is serving a 25-year jail term for corruption and rights abuses during a 1990s crackdown on leftist guerrillas.
