The decision yesterday further darkens the shadow over the reputation of Mr Moro and the sweeping “Car Wash” corruption investigation he presided over for years.
He sentenced hundreds of business and political leaders previously believed to enjoy impunity and transformed himself into one of Brazil’s best-known public figures.
Some hailed him as a hero while others accused him of being a zealot.
“In this case what is discussed is something that for me is key: everyone has the right to a fair trial, due legal process, and the impartiality of the judge,” Justice Carmen Lucia, who cast the tie-breaking vote, said.
Mr Moro quickly became Mr Bolsonaro’s justice minister.
The ruling followed a separate decision from Justice Edson Fachin on March 8 to annul Mr da Silva’s two convictions on the grounds he was tried in a court without proper jurisdiction and establishing that he could be retried in federal court in the capital, Brasilia.
Mr da Silva’s attorneys, Cristiano Zanin Martins and Valeska Martins, said in a statement that the decision was “historic and reinvigorating.”
“We proved that Moro never acted as a judge but as a personal and political adversary of former President Lula,” they said.
Mr da Silva is universally known as Lula in Brazil.
“We suffered all sorts of illegalities in the Car Wash, some of them described in the ruling that recognised the bias of the former judge, such as the illegal monitoring of our phones so members of the investigation could follow the defence strategy in real-time.”
The decision earlier this month cleared the way for Mr da Silva to face off against Mr Bolsonaro in the 2022 elections.
But legal experts also interpreted it as a means to head off a ruling on allegations of Mr Moro’s bias, and in so doing preserve the convictions and credibility of Car Wash.
Another justice called for a vote on the pending matter regardless.
With their 3-2 decision, the justices prohibited evidence gathered in the Car Wash probe about Mr da Silva’s alleged ownership of a three-floor apartment in the beach town of Guaruja from being used in any eventual trial.
The justices didn’t rule whether evidence gathered previously could be used when retrying Mr da Silva’s other conviction or in his other two unresolved criminal cases.
Michael Mohallem, co-ordinator of the Justice Centre of the Getulio Vargas Foundation, said the ruling brought any corruption proceedings against the former president back to square one and solidified his 2022 candidacy.
But it also provides a glimmer of hope for others who have been jailed.
“Lula will be able to say he was persecuted by a judge who wanted to convict him. For the political campaign, that’s very valuable,” Mr Mohallem added.
“The fear is that many inmates will present cases to annul their sentences. The ruling opens that discussion.”