Jurors were emotional afterward one appeared to be crying.
Defense attorney Rudy Bautista said there will be an appeal of the verdict based on a number of legal issues.
Dalton, who has been in custody throughout the trial, could be sentenced to up to life in prison on both convictions.
In 3rd District Court this week, the victim, now 22, said Dalton told her that having sex with 38-year-old Geody Harman was God's will. The woman said Dalton later promised her "great blessings" if she also had sex with him.
"He made me feel as if no matter what I did, I could never be right before God," she testified. "I tried so hard. ... There was always something bigger he wanted me to do."
Bautista, in closing arguments Thursday afternoon, said the woman waited years to report the rapes and has been inconsistent with her story ever since.
"When someone's story keeps changing, there's a reason," Bautista told the jury of seven women and one man. "They can't remember the lie they told."
Throughout the trial, Bautista has argued that the woman came forward with her story because she was angry with Dalton and wanted to ruin him financially. Bautista also said the woman was encouraged by others who wanted the church hurt.
Salt Lake County prosecutor Tupakk Renteria called those arguments "red herrings."
"She was raped at 15 years old by a person who should have protected her," Renteria said.
Dalton told the girl he was "the Holy Ghost" and church members called him "God in the flesh," officials said. The prosecutor said Dalton "served her up on a platter" to Harman, formerly the church's second in command.
Harman, who has been charged with rape, has been offered a plea deal that will allow him to plead guilty to a lesser charge and avoid further jail or prison time in exchange for his testimony, but he has yet to officially enter a plea.
The Church of the Firstborn of the General Assembly of Heaven left Utah and moved to Idaho before settling in southern Montana. The sect has never had more than 100 members.