Voting 8-6, the magistrates granted Solicitor General Jose Calida's quo warranto petition against Sereno.
Asked by reporters about her position in the Supreme Court after her press conference on Friday, Sereno said, "I haven't read the decision".
About 1,800 protesters gathered to support Sereno outside the court in Manila, where anti-riot police blocked an access road with trucks and iron railings to maintain order and separate a smaller group of anti-Sereno demonstrators.
Critics have said the SC and the House are in collusion with each other to prevent the Senate from convening into an impeachment court, which, according to Senate President Koko Pimentel, may ignore the quo warranto ruling.
Associate Justice Marvic Leonen stressed the landmark ruling "gravely diminishes" judicial independence and threatens the ability of the Supreme Court to uphold the people's rights.
"The ouster of our chief justice - this foundation of democracy, this shield against abuse of power in government - has crumbled", it said in a statement.
Her predecessor, Renato Corona, was impeached by the House in 2011 and became the first chief justice to be convicted in the 2012 Senate trial for failing to accurately disclose his bank deposits and properties.
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She has warned that the efforts by the Duterte administration to oust her are a threat to democracy, saying the petition that led to Friday's vote violates the constitution, which stipulates that top officials like her can only be removed by impeachment.
Her expulsion from the high court marks the first time that a chief justice was removed through a "quo warranto" plea, a legal recourse Sereno's camp had argued as incorrect.
The magistrates are scheduled start their deliberations at 10 a.m. Sereno, who terminated her indefinite leave of absence and reported back to work on Wednesday, said she would preside over the special en banc session but would inhibit when her colleagues start tackling the quo warranto petition. He says "the people should express to the court that the decision was wrong and unacceptable". She says she was ready to defend herself if the impeachment case reached the Senate for trial.
"I don't care about human rights, you better believe me", he said. In 2016, after Duterte accused some public figures and judges of being involved in the drug trade, Sereno angered the president by instructing judges not to turn themselves in to authorities before being presented with a warrant. "And you have to be out of the Supreme Court", Duterte said in a speech last month, in which he said he requested lawmakers to 'go into the impeachment right away'".
Sereno has denied any wrongdoing.
Other justices who voted to grant the petition were Associate Justices Teresita L. De Castro, Diosdado M. Peralta, Lucas P. Bersamin, Francis H. Jardeleza, Samuel R. Martires, Noel G. Tijam, Andres B. Reyes, Jr., and Alexander G. Gesmundo.
Global rights groups and local critics have accused Duterte of drifting toward authoritarianism after declaring martial law in the south amid a major attack by pro-Daesh militants previous year.