Christina Anderson, 44, and Ethan Anderson, 8, were allegedly killed by James DiMaggio. He then kidnapped the girl and was later shot to death by FBI agents.
The teen entered the church carrying a blown-up photo of her mother and brother. Their remains, and those of the family dog that was found shot to death in the burning house, were blessed by a priest during the public service.
Hannah and her father, Brett Anderson, also greeted friends and relatives, but left the eulogy to Christina's uncle.
"This was a national tragedy. It has been very painful. It has been unending pain and sorrow," said David Braun.
Braun said Hannah's safe return answered the family's prayers, and he praised the media and Amber Alert system for the role they played in her rescue.
DiMaggio's family has requested paternity tests to determine if the suspect fathered the children. Brett Anderson gave his DNA to investigators to confirm Ethan's identity. DiMaggio named Hannah's grandmother, Bernice Anderson, as the sole beneficiary of his employer-issued life insurance policy, making her eligible to receive $112,000.
Authorities have declined to discuss a possible motive in the deaths and haven't addressed other details of the case, including how Hannah was treated by DiMaggio during the ordeal.
The Associated Press contributed to this report.