The private Mass, held in the sloping foothills of the Sierra Nevadas, not far from Le's hometown of Placerville, came nearly two weeks after the 24-year-old graduate student's body was found hidden behind a wall in a Yale laboratory building in New Haven, Conn.
"We could ask a thousand whys for the rest of our life," said her pastor, Monsignor James Kidder.
Le's fiancé, Jonathan Widawsky, whom Le was to marry the day she was found dead, did not speak. He looked down somberly for most of the service, his father squeezing his shoulder, while Le's family members stood one by one to remember her.
Dan Nguyen, 15, Le's younger brother, said he loved his sister for "her silliness and friendliness." Whenever she returned home to visit, Nguyen said, Le and her siblings and cousins would play with stuffed animals and watch cartoons together.
Le never missed a birthday, Nguyen said, and would "send home presents on every occasion."
Le's mother, Vivian Van Le, read a poem she had written in Vietnamese after she "heard the bad news from New Haven."
In it, she recalled the lullabies she used to sing when her daughter was a child. Now that Le is dead, she said, she will sing a different sort of lullaby. Le's brother, Chris, 20, read an English translation of the poem.
The ceremony, held at the Holy Trinity Catholic Church in El Dorado Hills, was also filled with prayers and hymns. Much of the ceremony, including a rendition of "Amazing Grace," was in Vietnamese.
Le, a Yale graduate student in pharmacology, disappeared from a research building at the university's medical school complex on Sept. 8. Five days later her body was found stuffed into a crawl space inside a laboratory wall.
The state's medical examiner reported that Le died of asphyxiation. A lab technician, Raymond Clark III, was arrested on Sept. 17 and charged in her slaying. Police have not offered a possible motive. Clark has not entered a plea.
In the weeks since Le's death, her family has kept largely out of the media glare, even as the case captivated the nation. On Saturday, more than a dozen journalists from across the country stood outside of the ceremony.
In a statement to the media before the Mass, Kidder said the family hoped that the funeral would be "a chance for the family to come to reconciliation with something that is humanely irreconcilable: not only the fact that Annie died, but the way she died."
"There's a lot of mystery in this for me," Kidder added. He said that in an effort to understand Le's death, he had looked "to the center" of his faith.
Kidder fondly recalled the first time he met Le, then a high school student.
"It was a bunch of young kids," he said, "and she had the biggest smile."
Le graduated at the top of her class at Union Mine High School in El Dorado in 2003. She was the school's valedictorian, and was one of two students voted "Most Likely To Be the Next Einstein."
She received nearly $160,000 in scholarship money to attend the University of Rochester, where she studied cell and developmental biology. It was there that she met Widawsky, who is now a graduate student in physics at Columbia University in New York City.
The couple had planned to wed in Syosset, N.Y., on Long Island. Not far from there, at a synagogue where Widawksy's family worships, Le was eulogized at another service Wednesday.
Le, the daughter of Vietnamese American immigrants, was raised by an aunt and uncle she regarded as parents. Her uncle, Robert Nguyen, was the last family member to speak on Saturday.He thankedthe more than 600 people who attended the service, and he gave thanks for the "thoughts and prayers" from around the world.
"Our beloved Annie continues to live deep in our hearts as we remember her graceful smile and the fullness of life with which she lived," he said.
Not long afterward, the family trailed behind while eight pallbearers wearing white scarves, white gloves and white roses took Le's shiny poplar casket to a waiting hearse.
She was buried in nearby Rescue.