The Supreme Electoral Court will determine if President Dilma Rousseff's and Vice-President Michel Temer's campaign received donations from illegal sources.
The probe was requested by the opposition PSDB (Party of Brazilian Social Democracy) party.
Opposition accuses that construction firms donated money to the government, bribed politicians and the state oil company, Petrobras, to secure contracts.
The court ruled five to two to reopen the investigation.
Despite the fact that the decision is not lawfully binding, it could be utilized by the opposition to build a case for Rousseff's indictment in the Congress that is progressively antagonistic to the disliked leftist leader.
Congress will have the last word on the Rousseff case.
Opposition members of the parliament are excited about the ruling, which has been described as the beginning of the end of Rousseff government.
"The Rousseff administration is over. This decision buries this administration once and for all," said Rubens Bueno, a MP from the opposition PPS (Popular Socialist Party) party.
The government had previously requested to postpone the decision, asking for the removal of the judge leading the case for publicly revealing he intended to vote against Rousseff, but TCU denied the request on Wednesday.
The Rousseff’s administration has denied any wrongdoing.
Attorney General Luis Adams said he will appeal the court's decision with the Supreme Court.
"The game is not over yet," he told reporters after the ruling.