Archbishop Salvatore Cordileone performed the ritual before some 150 supporters before holding a special Mass inside St. Raphael Catholic Church and a march to a Planned Parenthood clinic, the San Francisco Chronicle reported.
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Cordileone says the ceremony was intended to drive out evil and defend the image of Serra.
San Rafael police say they arrested five people on vandalism charges for knocking over the statue on Monday, leaving just the feet attached to the base.
The statue is being repaired and will be returned.
The archbishop held a similar exorcism ceremony in San Francisco last June, when a statue of Junipero Serra was vandalized and removed in Golden Gate Park during protests for racial justice.
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Cordileone said prayers in Latin, remarking that "the experts in the field tell me that Latin tends to be more effective against the devil because he doesn't like the language of the church.''
Father Junipero Serra was an 18th-century Spanish missionary priest and the father of the California mission system.
The Franciscan priest has long been praised by the church for bringing Roman Catholicism to what is now the western United States.
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However, in converting Native Americans to Catholicism, critics say he forced them to abandon their culture or face brutal punishment.
Depictions of Serra have been protested and vandalized over the years, and Pope Francis' decision in 2015 to elevate him to sainthood reopened old wounds.
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More recently, protests focusing on the rights and historical struggle of Black and Indigenous people led activists to topple statues of Serra in San Francisco, Sacramento and Los Angeles.