The same jury that convicted him will now decide his sentence, which could be imprisonment for up to life.
That penalty phase of the trial was to begin Thursday afternoon following a short break.
After the verdict, Jeffs' standby attorney, Deric Walpole, told news reporters, "Any time there's a loss, we are disappointed."
Walpole added that it appeared Jeffs would continue to represent himself during the next portion of the trial.
Prosecutors said they would need about two days to present evidence pertaining to Jeffs' sentence, which can include other alleged bad acts.
The verdict followed some bizarre behavior by Jeffs the self-proclaimed prophet of the Fundamentalist Church of Jesus Christ of Latter-Day Saints during his opportunity to present a closing argument.
During the 30 minutes allotted to him, Jeffs stood silent for all but the final minutes, when he muttered some barely audible words, then sat down.
Emily Detoto, one of Jeffs' former attorneys, confirmed the one-sentence closing statement was, "I am at peace."
Jeffs had spent the first 20 minutes of his closing staring forward. He then turned his gaze toward the prosecutors and the jury. At the 24-minute mark, Jeffs uttered the four-word phrase. He sat down six minutes later.
When Jeffs' 30 minutes ran out, Walther declared the trial concluded and ordered the jury to begin deliberating.
During his closing statement, prosecutor Eric Nichols stressed to jurors that the so-called religious persecution and freedom issues Jeffs had raised in his defense should have nothing to do with their deliberations.
"This case is not about any people, not about any religion. This case is about Warren Steed Jeffs and what he has done," Nichols said.
Prior to closing arguments, with the jury out of the room, Jeffs made a motion to allow the jury find him innocent of based on "pure religious intent." Walther denied the motion.
After deliberating more than two hours, jurors asked to listen again to several audio tapes, one the prosecutors said was a recording of Jeffs having sex with the 12-year-old girl. The other two tapes are purportedly recordings of Jeffs instructing his wives, including the older girl, on how to please him sexually.
Jurors also asked for a transcript of the testimony of Rebecca Musser, a wife of former FLDS prophet Rulon Jeffs, who was Warren Jeffs' father. Musser testified that the FLDS faithful keep detailed birth and marriage records, and records of blessings they received, believing they must match records kept in heaven. Musser had testified for about three hours on Monday.
Walther told the jury that court rules do not allow them to see a transcript of Musser's testimony, but a court reporter could read Musser's testimony to them.
Earlier Thursday, Walther ended Jeffs' attempt at putting on a defense when Jeffs went three minutes without calling a witness.
Jeffs, who began his trial last week by firing his attorneys and then embarking on long, meandering discourses on polygamous beliefs mixed with dire prophecies of doom for the judge and prosecutors, had recalled FLDS member J.D. Roundy to the witness stand Thursday morning.
Roundy, who had testified about the sect's doctrines for four and a half hours on Wednesday, lasted 30 minutes on Thursday before Walther dismissed him.
Jeffs had continued to ask theological questions of Roundy, despite repeated objections by the prosecution which Walther upheld that the questions were irrelevant to the charges that Jeffs had sexually assaulted two girls.
Jeffs became silent when Walther dismissed Roundy. And when Jeffs failed to call a new witness, the judge declared he had rested his case.
Jeffs also asked the court repeatedly for continuances Thursday, saying that his "incarceration has limited me since 'pro se' defense was invoked. That is the simple truth." Walther denied the requests.
On Wednesday, Jeffs had asked Roundy to read selections from Mormon scripture and the writings of church founder Joseph Smith. The topics included the "everlasting covenant" of plural marriage, and the idea of a living prophet who is the voice of God.
"How many can hold this authority?" asked Jeffs, who is considered a prophet by the 10,000 or so members of the FLDS church. The mainstream Church of Jesus Christ of Latter-day Saints renounced polygamy more than a century ago.
"One at a time can, on this Earth" be the prophet, Roundy said. The former schoolteacher testified about his own faith in the FLDS Church's beliefs.
Prosecutor Nichols objected several times, saying that neither man's religious beliefs were relevant to the sexual assault charges.
Walther let Jeffs continue but admonished him to stay on topic.
Also Wednesday, the jury heard an audio recording of Jeffs purportedly having sex with the 12-year-old girl he is accused of taking as a wife with two other wives present and possibly participating.
Jeffs is heard panting and breathing heavily throughout the 21-minute tape recording. And while it was difficult to hear some portions due to background noise, a girl's voice occasionally can be heard and Jeffs twice refers to the victim by name.
The girl is not heard resisting, and there are no overt references to sex.
But prosecutors had earlier presented testimony that certain phrases heard on the tape are used by Jeffs and his followers to refer to sex, including "heavenly comfort" and "heavenly sessions."
Just before the tape ends, Jeffs is heard saying, "In the name of Jesus Christ, Amen."
And three female voices are heard replying, "Amen."
Throughout his defense, Jeffs never mentioned the sexual assault charges against him not even to proclaim his innocence.
Prosecutors say Jeffs "married" one of his victims when she was 14 years old. Jeffs got the girl pregnant when she was 15.
A DNA expert testified Monday there is a greater than 99.9 percent certainty that Jeffs is the father of the girl's baby.
Jeffs married the 12-year-old girl on July 27, 2006 at the FLDS's Yearning for Zion Ranch in Eldorado, Texas, according to records seized by police during a massive 2008 raid at remote ranch.
When Jeffs told the girl's father of the planned marriage, the father replied, "I am willing," and smiled, according to Jeffs' priesthood records. The father was present at the wedding ceremony.
Neither of the girls testified for the prosecution.