Le's mother, Vivian Van Le, read a poem she had written in Vietnamese that was translated by another brother, Chris Le.
"Farewell my child ... the most wonderful gift that God had sent to me," Le's mother said, going on to describe her daughter's death as being "like a knife searing through my soul."
The service at Holy Trinity Catholic Church in El Dorado Hills, about 30 miles east of Sacramento, follows a memorial service earlier in the week at the Long Island synagogue of Le's fiance, Jonathan Widawsky.
As about 600 mourners filed in Saturday, the church's pastor, Monsignor James Kidder, called the service conducted in English and Vietnamese "a chance for the family itself to come to reconciliation with what humanly is irreconcilable - not only the fact that Annie died but the way she died."
Kidder called Le "a rare person ... a person who is naturally good."
Le was busy but always had time for others, he said. "She was lots of fun and she had a wicked sense of humor."
Kidder had been Le's pastor until she graduated from Union Mine High School near Placerville and left for college. He said her family was seeking healing from Saturday's funeral and burial.
Lab technician Raymond Clark III has been charged with killing Le, 24, five days before her body was found on Sept. 13, the Sunday she was to marry Widawsky. She had been stuffed inside a wall in the basement of a research building in Yale's medical school complex.
"Jon, even now Annie's gone, but I still have you and love you very much. You are my son," Vivian Van Le told her daughter's fiance during a eulogy. Widawsky and members of his family attended Saturday's service but did not speak.
Le (pronounced "lay") was born to Vietnamese parents Hoang and Vivian Van Le in San Jose, according to a statement issued Friday by the university. He remarried after a divorce, but the university did not say where he or Le's mother live.
Le and her brother, Chris Le, a student at the University of California, Davis, were raised by an aunt and uncle near Placerville, in a home deep in the woods and miles from the nearest town.
They are described by the family as her "guardian parents." The guardians, Robert Linh Nguyen and Ngoc-Tuyet Bui, had three children of their own, including Dan Nguyen, whom Annie considered to be her brother.
Family spokesmen could not say when Le's parents came to the U.S. from Vietnam or why she was raised by her aunt and uncle.
Annie Le excelled in high school and took a special interest in science and medicine. She graduated as valedictorian in 2003, and classmates voted her "most likely to be the next Einstein."
Her drive led her to spend hours applying for college scholarships, eventually being awarded nearly $160,000 worth. She attended the University of Rochester in New York, majoring in bioscience, and met Widawsky, now a graduate student in physics at Columbia University.
Le began attending Yale as a graduate pharmacology student in 2007 and was on track to earn her doctorate in 2013. She was working on research with enzymes that Yale said could help with treating cancer, diabetes and muscular dystrophy.
"Hers were great achievements and there were more to come," Kidder said during the service. "She wanted to do the best and be the best to keep people from having their lives cut short. Ironic, isn't it, that her life was so sadly cut short."
Colleagues and family members said Le had an outsized personality and a determined will that belied her 4-foot-11, 90-pound frame.
"Although Annie was small in size, she had a large heart and a personality that filled the room," her laboratory colleagues wrote in the university statement. "No challenge ever seemed too large for her to overcome."
Yale officials are planning an Oct. 12 memorial service on campus and said they are establishing a scholarship in her memory.
