The 51-year-old won 50.135% of voters' support in the runoff, held on 7 June, to 49.865% for left-wing candidate Roberto Sánchez - a margin of less than 50,000 votes, figures certified by Peru's electoral court show.
It is the fourth time the daughter of disgraced former President Alberto Fujimori has sought the South American nation's presidency, promising this time to oversee a crackdown on organised crime.
Her election, coinciding with the election of Abelardo de la Espriella in Colombia, marks a shift towards the right in Latin American politics.
Fujimori said she would assume the role of president "with responsibility, humility and a deep sense of duty".
"Each day of this transition process is an opportunity to listen, engage in dialogue and arrive prepared at the start of the new government," she added, with what appeared to be a nod to her thin mandate.
Sánchez, 57, has alleged the runoff election had been "seriously compromised" and threatened legal action, arguing that strong support for Fujimori among Peruvian voters abroad was a sign of irregularities.
After the result was declared on Friday, his party appealed against the electoral court's proclamation, calling for the vote to be nullified.
While Sánchez, a former foreign trade minister, stood on a platform of broad economic reforms, Fujimori benefited from concerns over crime and political instability dominating the race.
Throughout the campaign, she leant on the controversial legacy of her father, promising a military crackdown on organised crime, in particular extortion incidents that have soared in recent years.
Alberto Fujimori was eventually jailed for crimes against humanity over extra-judicial killings and forced sterilisations undertaken during his increasingly authoritarian leadership.
