The controversial mayor arrived at the Central Jail just after 7 a.m. and was booked and released less than two hours later, according to San Diego County Sheriff's Lt. Dave Schaller. He had been scheduled to undergo the process Sunday.
The Democrat resigned less than two months ago after several women publicly accused him of sexual harrasment and unwanted advances.
Filner pleaded guilty to charges of felony false imprisonment and misdemeanor battery Tuesday.
The false imprisonment charge stems from a fundraising event in San Diego in March, when the 71-year-old mayor restrained Jane Doe 1 against her will.
One battery charge stems from a "meet the mayor" event in April when Filner kissed the victim on the lips without her consent. And the second battery charge was from an incident at the Fiesta Island Rally in May when Filner grabbed the victim's bottom without her consent while posing for a photo with her.
The plea agreement came on the same day Filner was charged in a criminal complaint by the state Attorney General's Office.
Filner faced up to four years in state prison, but under the plea agreement, Filner will serve probation for three years and home confinement for three months.
The agreement also bars Filner from ever seeking or holding public office again, and Filner will not be allowed to vote, serve on a jury or own a firearm while he is on probation due to the felony plea.
The plea agreement also requires that Filner undergo treatment as directed by a mental health professional during his probation. If he violates probation, he could face up to six months in jail.
His sentencing hearing is scheduled for Dec. 9.
The Associated Press contributed to this report.