A crowd of some 5,500 spilled into the streets surrounding the towering Crystal Cathedral, where a massive marble altar was bedecked with pink and white flowers and hearts.
A small closed wooden coffin with brass handles sat before the congregation, covered with flowers.
The cathedral was filled to capacity with people of all ages and races who came from all over.
Bells chimed to signal the start of the funeral service. There were several musical performances, including "Whenever I Feel Afraid" from "The King and I."
Mourners were given a program inscribed "Samantha Bree Runnion, 1996-2002" with a picture of the curly-haired girl superimposed on a cloud. Inside was a drawing by the slain girl showing a girl with a red dress and a house with a heart under a blue sky with the words, "Be Brave."
"Nothing can bring our baby back," said the girl's mother, Erin Runnion, choking back tears as she spoke at the funeral. "But knowing that her death was handled with the utmost integrity and her life cherished by so many does bring some solace. We are overwhelmed by the love people have shown Samantha. We always knew she had a gift for the world but it never occurred to us that her greatness would be realized in her death."
Mrs. Runnion also presented a slide show of Samantha's artwork accompanied by music from the movie "Peter Pan," which the little girl loved.
Samantha's father, Derek Jackson, flew in from Massachusetts for the memorial. Her 5-year-old friend Sara, who was the sole witness for the kidnapping, was also in the crowd, according to church officials.
A private burial service attended by family members and close friends was held after the funeral.
Though authorities say that no more children are being abducted this year than in the past, a series of high-profile cases involving unusual circumstances in the last six months have touched a nerve with the American public.
In June, still-missing Elizabeth Smart, 14, was taken from her bedroom in Salt Lake City, Utah by a man with a gun as her sister feigned sleep. In February, Danielle van Dam, 7, vanished from her bed in a San Diego suburb. Her body was found three weeks later. A neighbor, 50-year-old David Westerfield, is on trial in her murder.
And in Oregon, two teenage girls who live in the same apartment complex were snatched - two months apart - apparently from the same road. Ashley Pond, who was abducted in January and Miranda Gaddis, who vanished in March, are both still missing.
In Anaheim Wednesday, officials at the Crystal Cathedral, a spectacular glass-walled church which hosts the internationally televised "Hour of Power," installed loudspeakers to accommodate mourners who would not fit inside the 2,800-seat church or in an overflow area, which holds another 1,000 people, for Samantha's funeral.
"I think Samantha's death has touched everybody's lives," said church spokeswoman Bonnie Balloch. "They feel like this is something they can do."
"It's not fair that we're looking at a tiny little casket," the Rev. Robert A. Schuller II told those in attendance. "It's not fair. It's wrong. What is good is what brought all of you here today ... Love, support, community."
Orange County Sheriff Michael Carona, who headed the massive search for Samantha's killer, recalled the child's mother giving him a picture of the girl and a toy tiger, her favorite stuffed animal.
"Little girls aren't supposed to die," Carona said. "Little girls aren't supposed to die the way Samantha died."
At the end of the service, mourners applauded in a show of support as the family followed the casket out the church, then lined streets and walkways as the processional left cathedral grounds.
Many of those present said they saw Samantha as one of their own.
"It could have been in our neighborhood, it could have been one of our children," said Lisa Genera, 23, of Anaheim, who brought her 3-year-old daughter Ashley to the service.
"She doesn't understand killing, so I told her (Samantha) was up in heaven," Lisa Genera said. "She understood that."
Samantha was playing the board game Clue outside her house on July 15 when a man drove up and pretended to be looking for his lost Chihuahua puppy before snatching the girl and speeding away.
Her naked and bruised body was discovered the following day, left by the killer on a lonely stretch of two-lane mountain road about 50 miles (64 km) away. Authorities said she had been sexually assaulted and suffocated to death.
Meanwhile published reports said police were using credit card and cell phone records to smash the alibi of Alejandro Avila, the 27-year-old factory worker accused of killing Samantha, and show that he was in the area where her body was found just hours after the kidnapping.
Avila, who lives about ten miles from the spot where the body was found, was arrested on July 19 and charged with kidnapping, two counts of sexual assault and murder that could bring him the death penalty if he is convicted.
Authorities say Avila - who was acquitted in neighboring Riverside County last year of molesting the 9-year-old daughter of his then-girlfriend and another girl the same age - was familiar with the apartment complex where Samantha lived.
Sources close to the case have told Reuters that one of the girls, who is now 11 or 12, lived with her father at the apartment complex until recently and knew Samantha.
Avila, who is being held without bail pending his arraignment on the charges, has reportedly told police that he was shopping at a mall some 30 miles away from Samantha's house at the time she was abducted.
But police have questioned that alibi and the Los Angeles Times reported in Wednesday's editions that Avila's cell phone and credit card records suggest he was in the area where Samantha's body was found just hours after the kidnapping.
The paper also reported that preliminary tests of fibers found on Samantha's body appeared to match fibers from two vehicles that Avila was known to drive.