The court is hearing cases involving top suspects in a vast corruption scandal linked to state oil firm Petrobras, which has snared numerous politicians including allies of Temer.
A new judge had to be found after the death of Teori Zavascki, who was helping lead investigations into politicians implicated in the scandal.
The Senate in a vote approved by 55 votes to 13 the appointment of Temer's former justice minister Alexandre de Moraes, 48, the chamber's speaker Eunicio Oliveira announced.
During questioning by senators on Tuesday he promised to "act with absolute independence and absolute impartiality."
The cases Zavascki was handling have already been transferred by lot to another judge, so De Moraes will not take them on.
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