The Spanish-language funeral service for Suzie Pena drew about 150 people, including new Mayor Antonio Villaraigosa.
Protesters have staged nightly demonstrations since the July 10 shooting, heckling police and waving signs calling officers involved in the shooting "baby killers."
The toddler was used as a human shield by her father, Jose Pena, 34, who also was killed by police when a SWAT team raided his business following a 2½-hour standoff that left one officer wounded.
The Rev. Jose Valdez Romo did not mention the role of police or the girl's father in the toddler's death during the service.
Lorena Lopez led the pallbearers who escorted her daughter's small, white casket out of the church. She shakily kept her right hand on it as tears streamed down her face. Lopez's 16-year-old daughter, who escaped from her stepfather during the standoff under the cover of police gunfire, was among the pallbearers.
Outside the church, a man shouted in Spanish that "the police are assassins" as the casket passed by.
Villaraigosa, who arrived at the church midway through services, embraced Lopez and her family during the part of the Mass when parishioners greet each other and offer a peace blessing.
"All of us grieve with the family," the mayor said after the service.
Villaraigosa, the city's first Latino mayor in more than a century, also promised a thorough investigation.
"We will do everything possible to make sure we uncover every fact," he said.
Suzie Pena was only the second hostage to be killed by SWAT team officers in its 38-year history. Members of the team have been traumatized by the incident and have received counseling, police said.