The election pits leftist President Luiz Inacio Lula da Silva against right-wing Senator Flavio Bolsonaro, the son of convicted former President Jair Bolsonaro.
Polls were initially set to close at 5pm on Sunday Brasilia time (7am Monday AEDT) and will now close at 7pm, after Supreme Justice Cristiano Zanin 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 5pm cutoff, when the electoral court had already started publishing results that showed Lula leading Bolsonaro with 0.25 per cent of ballot counted.
Lula had 57.66 per cent of votes, compared with 42.34 per cent for Bolsonaro, the early count showed.
After the Zanin ruling, the TSE said it would pause the vote count to allow for the extended voting window to close.
The pause over the vote count injects uncertainty into a Brazilian electoral process still grappling with the fallout from 2022, when Jair Bolsonaro refused to concede defeat to Lula.
His supporters later invaded government buildings in protests against the result, and Bolsonaro received a 27-year prison sentence for plotting a coup.
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.
Bolsonaro had also asked for voting to be extended in at least three states, citing bad weather.
with AP and dpa
