The court denied a request by Alioto-Pier for an emergency review of a recent appeals court ruling against her.
The decision means that Alioto-Pier cannot run for re-election in District 2 in November and will be termed out of office in January.
"While I am disappointed in the outcome, I of course respect the judicial process," Alioto-Pier said in a statement. "I will continue to work hard for the residents of my district and the people of San Francisco for the remainder of my time in office."
District 2 covers many of the City's northern neighborhoods, including the Marina, Cow Hollow, Pacific Heights, Russian Hill and part of the Richmond District.
Alioto-Pier, who has served nearly seven years as supervisor, had claimed that, because she was initially appointed to the position by the mayor, her first term should not count under the City charter's two-term limit for supervisors.
City Attorney Dennis Herrera opposed her position, and although a superior court judge ruled in Alioto-Pier's favor on July 22, a state appeals court reversed the decision on Aug. 24, saying she had already served two full terms.
"Michela Alioto-Pier is someone I've regarded as an ally on important issues, from protecting public safety to fighting to shut down the Mirant power plant," Herrera said in a prepared statement this afternoon.
"While we obviously disagreed on the interpretation of the City's term limits law, I have always respected her right to pursue this dispute in court," Herrera said.
Herrera had argued that the voter-approved term-limit rule had a provision that if an appointed supervisor serves more than two years of a term, it should be rounded up to count as a full four-year term.
Alioto-Pier, however, said, "I believed and continued to believe that the intent of the voters as reflected in the plain language of our city charter allows me to run for second four-year term."
Mayor Gavin Newsom appointed Alioto-Pier to replace him as District 2 supervisor in 2004 after he was elected mayor.
Alioto-Pier then won an election in November 2004 to serve out the remaining two years of the four-year term and was re-elected to another four-year term in November 2006.