The felony count alleges false imprisonment "by violence, fraud, menace and deceit" but does not elaborate on the circumstances. The three victims were not identified.
Filner, 71, resigned in late August, succumbing to intense pressure after at least 17 women brought lurid sexual harassment allegations against the former 10-term congressman.
He had been on the job less than nine months into a four-year term and was San Diego's first Democratic mayor in 20 years.
Filner's former communications director, Irene McCormack Jackson, was the first woman to go public with allegations against Filner and filed a lawsuit against the mayor and the city, claiming her ex-boss asked her to work without panties, demanded kisses, told her he wanted to see her naked and dragged her in a headlock while whispering in her ear.
All nine City Council members as well as fellow Democrats called upon Filner to resign. A recall effort also was launched as more allegations surfaced.
In exchange for his resignation, the city will pay Filner's legal fees in a joint defense of the lawsuit, and cover any settlement costs assessed against the mayor except for punitive damages.
The city as required by state law will also defend Filner against legal actions stemming from other alleged sexual harassment said to have occurred during his nine months in office as mayor.
City Attorney Jan Goldsmith said, however, the city will not represent Filner in any criminal case.
