Mehserle, 28, was convicted of involuntary manslaughter for the shooting death of unarmed passenger Oscar Grant III at the Fruitvale station in Oakland on Jan. 1, 2009.
Hundreds of people staged a protest the night the verdict was announced.
The lawsuit, filed in Alameda County Superior Court, named Gerald Dugas, of Castro Valley, and Oakland residents Paul Rousseau, Raquel Sharp and Terry Williams as defendants.
Rousseau and Sharp were arrested after Oakland police officers filmed them spray-painting graffiti on public property, according to the lawsuit.
Rousseau also tried to punch an undercover officer and attempted to steal the officer's camera, according to an Oakland police report cited in the suit.
It also alleges that in the midst of the protest, a crowd broke through the security gate at JC Jewelry at 1940 Broadway, kicked in a window, punched one of the owners in the face, and made off with more than $50,000 in property.
The suit says the jewelry store's owners "suffered economic and emotional harm" and feared physical harm as they tried to fend off a crowd of more than 200 people.
According to Oakland police, Williams was seen looting the store with other suspects, and both Dugas and Williams were caught with gold jewelry stolen from the store.
The lawsuit seeks a total of $100,000 from Dugas and Williams and unspecified punitive and graffiti-related damages from Rousseau and Sharp.
City Attorney spokesman Alex Katz said the four defendants have already been charged with criminal offense but are also being sued by the city.
"It's a way for us to stand up for the business owners in town and people who want to come here and engage in peaceful protest," he said.
California law allows the city to bring the lawsuit action to protect business owners' rights to exclusive possession of their property, City Attorney John Russo said. Any recovered penalties will be awarded to impacted businesses.
Although many people engaged in looting and vandalism on the night of the protest, the city is only suing the four defendants at this point because it has the strongest evidence against them, including videotapes, Katz said.
He said the city is concerned that people wanting to engage in peaceful protests in the future might be dissuaded from participating if they fear that the protests will spiral out of control and result in looting and vandalism.
"When people use a protest as an excuse to destroy property, it has a chilling effect on dissent," Katz said.
Russo said in a statement that Oakland has a long tradition of non-violent protest and dissent, but on July 8, some people "disrespected that tradition" and treated the city like a "lawless playground."
"The individuals who set fires, assaulted journalists, robbed local business owners and incited chaos were not here for justice," he said. "Sadly, it appears they were here for no other reason than to get an emotional rush from destruction of property, theft and lawlessness. Oakland will not tolerate this disrespect."
Alameda County District Attorney spokeswoman Teresa Drenick said Williams, 33, pleaded guilty to a felony charge of violating his parole for a previous conviction for possession of marijuana for sale. She said he was sentenced to probation, including one year in the county jail.
Drenick said Rousseau would have a preliminary hearing on Monday on a felony attempted robbery charge.
She said Dugas faces a felony commercial burglary charge, and Sharp faces a misdemeanor vandalism charge.
Mehserle is scheduled to be given a sentence next week ranging from probation to as much as 14 years in state prison.