The woman said she was 8 when Jeffs summoned her to his office and asked her to sit on his lap. She did not specify what Jeffs did to her but made it clear it was molestation.
"I didn't know I was supposed to tell him no," the woman told the jury.
The trial has attracted court watchers from across west Texas. A few observers in the gallery cried with her.
The woman said she did not disclose the abuse until she met Texas rangers who traveled to Utah to investigate Jeffs following the 2008 raid on the Yearning for Zion Ranch in Eldorado.
A jury is considering whether Jeffs, 55, should spend up to life in prison. The jury on Thursday convicted the polygamous sect leader of aggravated sexual abuse of a child and a count of sexual abuse of a child for having sex with 12- and 15-year-old girls he took as celestial wives.
Prosecutors are introducing evidence of so-called other "bad acts" committed by Jeffs since at least 1989.
The jury also heard Saturday from Brent Jeffs, Warren Jeffs' now 28-year-old nephew. The man was in tears as he told Texas District Court jurors about being raped by his uncle when he was 5.
He said Jeffs pulled him aside at a family meeting, took him into a restroom, ordered him to kneel like he was praying, then raped him.
"He told me this was God's will, this was God's work," the nephew said.
Warren Jeffs also warned the boy that, "this is between me and you and God and no one else needs to know about it."
The Tribune does not typically identify victims of sexual assault. However, Brent Jeffs has been public about the allegations against his uncle.
In 2003, he sued Warren Jeffs but settled out of court for 3 acres of land in the FLDS' Utah-Arizona border community.
Jurors also heard testimony from Texas Ranger Brooks Long, who described finding plans for a table that could be transformed into a bed during a 2008 raid in the FLDS temple at the YFZ Ranch.
Long said rangers found a bed with chairs around it in one room of the temple and another disassembled bed stored in a closet.
Investigators then unearthed a document, dated May 30, 2005, and allegedly drafted by Jeffs, that detailed construction of the table-bed, which had a removable top, underneath which was a mattress.
Jeffs also gave instructions to put a plastic cover over the mattress "to protect the mattress from what will happen on it," Long said, quoting from the document.
While the document never specifies that Jeffs planned to engage in sex on the table-bed, prosecutors have already presented evidence Jeffs had sex with underage girls in the temple.
Life changed dramatically in the FLDS Church after Warren Jeffs took control, a former member testified Saturday.
"The festivals, the parades it all came to an end," Ezra Draper told the jury. "Movies were banned."
Draper left the FLDS community in 2003, but continues to live in Hildale, which, along with its sister town of Colorado City, Ariz., comprises the primary FLDS community.
Jeffs' father and predecessor, Rulon Jeffs, was an agreeable man whom you could approach, Draper testified. But when Rulon Jeffs' health began deteriorating in the early 1990s, he began delegating more authority to Warren Jeffs, and the younger Jeffs took his on own initiatives in his father's name.
Among the changes was ending the annual Pioneer Day parade in Hildale and Colorado City as well as ending the towns' fall harvest festival, Draper said. Warren Jeffs ordered televisions removed from homes, forbade people from installing Internet connections and prohibited magazines as benign as Motor Trend, Draper testified.
On Jan. 30, 2004, Warren Jeffs evicted Draper's brother, David Draper, from Hildale and Colorado City and took away his wife. A document prepared by Warren Jeffs said David Draper needed to "clean up" his life. Outside the courtroom, Ezra Draper told a reporter his brother was evicted because he suffered from schizophrenia.
David Draper killed himself on July 21, 2006, and Ezra Draper attributes the suicide to the eviction from Warren Jeffs, which eliminated his brother's support system.
Ezra Draper hopes the jury gives Warren Jeffs life in prison.
"He has never been made accountable for his bad choices, and this is his accounting," Ezra Draper said outside the courtroom.
Court will resume Monday at 8 a.m. Utah time with the prosecution still presenting evidence. Then it will be the defense team's turn to present.
Jeffs was not in the courtroom Saturday. On Friday, he told Judge Barbara Walther he did not want to be present for the proceedings and did not want an attorney to represent him. Walther allowed Jeffs' absence but said Texas court rules do not allow a defendant to be unrepresented. Jeffs had been acting as his own attorney, but his standby lawyers assumed his place Friday.