The judge refused to find Jeffs in contempt of court during a hearing in St. George, Utah.
Wendell Musser sued Jeffs to learn the whereabouts of his wife and son.
Musser claims Jeffs forced him out of the Fundamentalist Church of Jesus Christ of Latter Day Saints and cut him off from his family last summer after a drunken-driving arrest in Colorado.
The judge said the dispute between Barlow and his wife over their 2-year-old son should be left up to the parents and court — not Jeffs.
Both parents are seeking sole custody of the boy.