Brazilian right-wing Senator Flavio Bolsonaro overtook President Luiz Inacio Lula da Silva in Brazil's tightly contested presidential runoff on Sunday evening, as results trickled in after a Supreme Court-mandated pause in vote counting injected confusion into an already tense runoff race.

A woman looks at the printed results from a ballot box at a polling station in Jacarepagua, in the southern zone of Rio de Janeiro, Brazil, during the presidential runoff election on October 25. (AFP)

With over 20% of tallies reported, Bolsonaro, the son of convicted former President Jair Bolsonaro, led with 50.02% to Lula's 49.98%.

A victory for Bolsonaro, 45, would extend a wave of right-wing victories for Latin American candidates friendly to US President Donald Trump, while a fourth mandate for Lula would be a bulwark against Washington's influence in the region as his government has pushed back on US trade and security policies.

Yet the contest threatens to be overshadowed by legal disputes after Supreme Court Justice Cristiano Zanin, who was formerly Lula's lawyer, accepted a request by Lula's campaign to extend voting, pointing to public transportation issues in three cities in the state of Bahia.

Zanin's decision landed right around the election's 5pm local time cutoff, creating confusion as some polling stations had already closed.

In a subsequent ruling, Zanin said those stations would remain shut, allowing authorities to begin tallying those votes, but that polling stations that had not closed after the official cutoff could keep receiving voters for an additional two hours.

Zanin's ruling led the electoral court, or TSE, to pause the count for two hours.

Also read: Brazil presidential race heats up as Lula, Bolsonaro seek each other's disqualification over social media row

Two legal experts told Reuters the extension of voting hours and allegations around disrupted public transportation could draw legal challenges.

“Depending on the election result, there is a possibility that the losing side might attempt to contest the outcome, arguing that many people were unable to vote even with the extended deadline," said Vera Chemim, a constitutional lawyer in São Paulo.

The senator's brother Eduardo Bolsonaro, speaking on a live stream on his YouTube channel, questioned why the Supreme Court had ruled in a process overseen by the country's federal electoral court: "Strange, isn’t it?" he said. "It’s hard to imagine what the legal basis for this could possibly be. It doesn’t inspire credibility.”

Lula had asked electoral authorities to extend voting in at least nine states after his campaign alleged some officials reduced election-day public transportation, impacting voters' ability to get to the polls.

Earlier on Sunday, a court in Bahia, a Lula stronghold in the Northeast, ordered the arrest of a top transportation official in the city of Salvador over allegations that he directed a reduction in the city’s bus fleet.

In comments before Zanin's decision, Lula said "something abominable is happening" in this election.

Also read: US influence, personal attacks: Brazil's Lula, Bolsonaro clash in heated debate ahead of run-off vote

Flavio Bolsonaro had also asked for voting to be extended in at least three states, citing bad weather.

Reuters on Saturday revealed a campaign within Trump's State Department to help get the Bolsonaros back in power.

Trump has so far declined to endorse a candidate. Asked on Sunday who he hoped would win, Trump declined to say.

"I don’t want to get into that, but we are watching," he told reporters in Washington.