Keiko Fujimori, a conservative and daughter of a disgraced former president, and Roberto Sánchez, a nationalist congressman, beat 33 other candidates in the first round in April, but neither earned even 20 per cent of support.
Pollsters estimate that roughly 30 per cent of voters remained undecided.
Sunday's results were expected to be tight, and the outcome may not be known for days.
Electoral authorities took more than a month to declare Fujimori and Sánchez the winners of that vote.
Voting is mandatory for Peruvians aged 18 to 70. More than 27 million people are registered, and of those, about 1.2 million are expected to cast ballots from abroad, mainly in the United States and Argentina.
Official results from April's election showed Fujimori received 17 per cent of the vote and Sánchez got 12 per cent. More than six weeks later, a nationwide poll conducted by Ipsos found that similar shares of voters were supporting the candidates, with about three in 10 saying they were undecided.
Fujimori is linked to the authoritarian and corrupt legacy of the government of her late father, Alberto Fujimori, in the 1990s. She became Peru's first lady in 1994 after her parents' separation.
Sánchez is one of the closest allies of jailed former president Pedro Castillo, whom many perceive as corrupt and chaotic. Castillo's 16-month term saw more than 70 Cabinet changes.
For most of her fourth presidential campaign, Fujimori promised to crack down on crime.
Her proposals include implementing technology to track extortion, militarising borders and increasing the presence of police and military personnel in high-risk areas. Fujimori, 51, has also said that prisoners will be required to work and "repay society".
In the only debate before the runoff, Fujimori defended her father's government and promised to defeat crime just as he defeated the Shining Path, a violent extremist group.
Sánchez, a former minister now popular with rural voters, has pledged to combat corruption within the police force and promote reforms that would enable the military to support security efforts.