Jagir Kaur was replaced by Jagdev Singh Talwandi, 78, as chair of the Sikh Shrines Management Committee in a unanimous vote, including Kaur's own.
Opposing factions wanted Kaur, who belongs to the governing Akali Dal party, removed from the religious post.
The meeting, attended by 165 of the committee's 180 members, was held at the Sikh community's holiest shrine, the Golden Temple, in Amritsar, 240 miles north of New Delhi.
Federal investigators have questioned Kaur over charges of murdering her teen-age daughter, conspiracy, covering up evidence, and causing the death of an unborn child without the mother's consent.
She is free on bail, an unusual circumstance in a murder case.
Kaur has said she is innocent.
Her son-in-law, Kamaljit Singh, says he married Kaur's daughter, Harpreet, 19, secretly in March and when Kaur found out about it, she lured her daughter to a clinic where an abortion was performed in April. Harpreet died 10 days later of what her mother said was food poisoning. No autopsy was conducted before her cremation.
In October, police in northern Punjab state charged Kaur and six others with murder, saying Harpreet's death was caused by sleeping pills added to her food.
The Sikh faith, founded in 1469 to counter the Hindu caste system, has often been at odds with the country's rulers. Sikhs are about 2 percent of India's 1 billion people. Their men take ``Singh,'' meaning lion, as part of their name, and the women take ``Kaur,'' or lioness.