Vassilios Skouris of Greece, a former president of the European Court of Justice, was elected head of FIFA's ethics committee on Thursday.
Taking over from German Hans-Joachim Eckert, who was instrumental in bringing down ex-FIFA president Sepp Blatter and UEFA chief Michel Platini, Skouris will serve a four-year mandate.
Colombia's Maria Claudia Rojas was also elected to take over from ethics investigator Cornel Borbely.
The controversial move to replace Eckert and Borbely was overwhelmingly approved by the annual FIFA Congress, meeting this year in Bahrain, with 97% voting for and just 3% against.
Eckert was the judge who opened proceedings against Blatter and Platini in November 2015, after FIFA was engulfed by accusations of corruption.
He also opened the case against Jerome Valcke, Blatter's former powerful deputy, which ended with the once all-powerful French administrator being banned from the game.
The replacement of Eckert and Borbely has raised concern in some circles and critics have accused current FIFA president Gianni Infantino of having a personal motive to replace the pair, as an ethics investigation was launched against the world football's top powerbroker last year.
Adding to the drama of the last-minute removal of the ethics team, the pair arrived in Bahrain on Tuesday night to find out their four-year contract would not be extended.
They then held a hastily-arranged press conference in Manama on Wednesday, claiming their removal was a setback to the reform agenda and there were still several hundreds of cases of corruption outstanding, before immediately flying back out of the country.
"The removal means nothing else but the end of the reform process," Borbely told reporters.
But Infantino shrugged off the apparent crisis as a "storm in a teacup".
He said no one had been "removed" but that both Eckert and Borbely had simply come to the end of their terms.
"I certainly have no issue with Mr Borbely and Eckert," said Infantino.
However, he took a swipe at the pair with regards to the outstanding number of corruption cases.
"I think it's bad... that there are hundreds of cases that are still outstanding and have not been dealt with," he said.
Asked if he was under investigation, Infantino said he had "no idea".
In further nominations, Finland's Olli Rehn, former vice-president of the European Commission, was elected vice-president of the governance committee.
The president of that committee, former Portuguese cabinet minister Miguel Maduro, quit his job after just one year.
Related Story