Judge Eduardo Rocha Penteado ordered the suspension of the elevation of Temer's close ally Wellington Moreira Franco -- currently infrastructure investment secretary -- to minister status in the administration.
The nomination was controversial because Moreira Franco has been named in plea bargain testimony by former executives in the Odebrecht construction giant as taking part in illegal campaign funding.
Once becoming a minister, Moreira Franco's case would have automatically been transferred to the Supreme Court, which deals with sitting politicians, meaning they do not have to face prosecution in lower courts.
In his decision, Rocha Penteado cited the precedent of a similar case last year in which Temer's leftist predecessor Dilma Rousseff tried to bring her own predecessor, Luiz Inacio Lula da Silva, into the government.
That move was widely seen as an attempt to shield Lula, who was embroiled in his own graft probe. It also ultimately failed and the former president now faces trial in lower courts.
Brazilian politics has been shaken to its roots by revelations of a far-reaching embezzlement and bribery network in which political parties were funded with bribe money.
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