"Brazil cannot continue for another four years like this. Everyone's life has become worse," Bolsonaro said after casting his ballot in Rio de Janeiro, calling for political change.
Lula, who turns 81 in the coming week, is seeking a fourth presidential term and has presented his campaign as a defence of democratic institutions and national independence.
The election is also being watched for its implications for Brazil's relationship with the United States, where President Donald Trump has maintained close ties with the Bolsonaro family.
Flávio Bolsonaro has sought to distinguish his political style from that of his father, former President Jair Bolsonaro, while retaining the support of voters who backed the previous right-wing administration.
Jair Bolsonaro is serving a 27-year prison sentence following his conviction over an attempted coup after losing the 2022 presidential election to Lula, according to the AFP account.
His son has promised to secure his father's release as his first action if elected. He has also proposed pursuing the impeachment of Supreme Court Justice Alexandre de Moraes, who oversaw proceedings against the former president.
The former president's political legacy has remained a central issue throughout the campaign.
Supporters of Lula have organised demonstrations opposing the Bolsonaro family's return to power, criticising Jair Bolsonaro's handling of the COVID-19 pandemic, environmental policies and reductions in public services.
Economic concerns dominate campaign
Lula returned to the presidency in 2023 after defeating Jair Bolsonaro in the 2022 election, promising to rebuild social programmes and improve living standards.
His administration has overseen reductions in inflation and unemployment, alongside efforts to reduce hunger and protect lower-income households.
Nevertheless, concerns about the cost of living and public security have featured prominently in the election campaign.
Bolsonaro has appealed to voters frustrated by crime and government spending, while Lula has defended welfare programmes that he argues are essential to reducing poverty.
Walter dos Santos, a 56-year-old resident of north-eastern Brazil, told AFP that government assistance had made a substantial difference to families experiencing hardship.
The region has traditionally been an important source of electoral support for Lula, whose political career has been closely associated with programmes aimed at reducing poverty.
Critics of the president argue that public expenditure needs tighter control, creating a disagreement over the future direction of Brazil's fiscal and social policies.
Environmental policy has received comparatively limited attention during the campaign, despite renewed concerns about fires in the Amazon rainforest.
Deforestation in the Amazon has fallen to its lowest level in four decades under Lula, according to the AFP report, although recent fires linked to El Niño conditions have affected communities across the region.
Campaigns clash over social media
The contest has also extended to online platforms, where both candidates have sought to reach voters through digital campaigning.
Following his first-round defeat, Lula changed his social media strategy, recording more personal videos and increasing his direct engagement with online audiences.
His campaign accused Meta, the company behind Facebook, Instagram and WhatsApp, of algorithmic manipulation that it said disadvantaged his election advertising.
Meta denied favouring Bolsonaro but acknowledged that some advertisements associated with Lula's campaign had been incorrectly suspended because of technical problems.
The controversy added another point of disagreement to a campaign already shaped by economic concerns, public security and disputes over Brazil's democratic institutions.
Political analyst Thomas Traumann warned that either candidate could face serious institutional challenges after the election.
He said a Lula victory could produce confrontation with a Congress strengthened by right-wing electoral gains, while a Bolsonaro presidency could intensify tensions with the Supreme Court.
The election will determine whether Lula remains in office for another four years or whether Flávio Bolsonaro becomes president, with the composition of Congress expected to shape the next administration's ability to govern.