Ricardo Berzoini, who had earlier stepped down as Luiz Inacio Lula da Silva's campaign manager but stayed on as party president, said he was resigning the presidency to maintain party "unity and cohesion".
Da Silva failed to win more than 50 per cent of the vote last Sunday and now faces a run-off on October 29 against Geraldo Alckmin, former Sao Paulo state governor, and his Brazilian Social Democracy Party (PSDB).
On Friday evening, officials also said the party would expel all members involved in the scandal, in which senior leaders are accused of trying to buy information that apparently incriminated a rival politician in a different scandal.
Berzoini had come under pressure to step down to distance da Silva from the corruption allegations before the run-off vote.
On Friday, Berzoini said he supported an investigation into the allegations and denied any involvement, although one of his subordinates has been implicated.
"I reaffirm that I never promoted or agreed with any form of illegality or irregularity in matters under my responsibility," Berzoini said.
He said he may return as party president after the investigation.
Workers Party officials said Berzoini would be replaced by Marco Aurelio Garcia, a former adviser and current campaign manager for da Silva.
A recent survey on Brazilian television indicated that da Silva would win 54 per cent of the run-off vote, compared with 46 per cent for Alckmin.