Projections by three polling firms, including the Ipsos-Apoyo firm in Lima, gave Humala -- a former military commander who ran for president in 2006 only to lose in a runoff -- a 3 percentage point victory over Fujimori.
Fujimori is the conservative daughter of imprisoned ex-President Alberto Fujmori, serving a 25-year prison sentence for a civilian massacre committed during a war with guerrillas during his presidency in the 1990s.
The non-governmental electoral watchdog Transparencia also indicated Humala would win by 3 percentage points -- 51.5 percent to 48.5 percent for Fujimori.
Fujimori, appearing briefly before supporters 5 hours after polls closed, did not concede defeat and asked them to "wait responsibly and with prudence" for the complete official results, due later Monday, Lima's America Television reported.
With 81 percent of the vote counted, Humala had 50.7 percent of the vote, while Fujimori had 49.3 percent, incomplete official results indicated.
Humala's lead widened after midnight Monday as later results were counted. The early results were weighted toward Lima and other urban areas, where Fujimori was strong, in contrast to rural zones reporting later, where Humala had more support.
Peruvians voting abroad, who account for about 3 percent of the electorate, favored Fujimori by a more than 2-to-1 margin, incomplete results from Peru's electoral commission indicated.
Humala, 48, vowed in his Lima victory speech to give poor Peruvians a greater share of the country's mineral wealth and said he would make Peru's dynamic economy "the great motor of the social inclusion that Peruvians desire," America TV coverage showed.
Peru is one of Latin America's star economies, enjoying 12 consecutive years of growth.
Humala, whom enemies likened to radical socialist Venezuelan President Hugo Chavez, has terrified Peru's traditional elite, the Los Angeles Times reported.
They will likely pressure him to quickly reveal his choices for key government positions, such as prime minister and economy minister, The Wall Street Journal said.
By contrast, many Peruvians saw Fujimori as a proxy for her authoritarian father, the Times said.