Harry Roque, a spokesman for Mr. Duterte, said Friday’s ruling was final.
“The Supreme Court is the final arbiter of the law,” he said. “The high court has spoken.”
In March her fellow justices asked Ms. Sereno to go on leave while the impeachment complaint was dealt with, and she complied.
But she returned to the bench on Wednesday, surprising everyone, and announcing that she would preside over court proceedings on Friday while abstaining from voting.
Ms. Sereno was appointed in 2012 by Benigno S. Aquino III, the predecessor of Mr. Duterte, who took office in 2016 on a promise to cut rampant crime by killing thousands of addicts.
As chief justice, she publicly clashed with Mr. Duterte, questioning his so-called watch list of drug suspects that contained the names of 150 local officials, police and military officers, as well as judges. At least three mayors Mr. Duterte has named as being in the list were later fatally shot in law enforcement operations. The police have defended those actions as legitimate.
Ms. Sereno had cautioned the president about the list, and she expressed her concern in a letter, which the president took as a slight.
She had also advised judges who were on the list not to turn themselves in unless a warrant was properly issued. A judge whose name was included was later found out to have died long ago, raising questions about the accuracy of Mr. Duterte’s list.