The Fundamentalist Church of Jesus Christ of Latter Day Saints leader was handed the maximum sentence possible.
Last Thursday, the 55-year-old was found guilty of forcing two girls into "spiritual marriages" and fathering a child with one of them.
The charges followed a raid on a remote west Texas ranch in 2008.
Jeffs stood quietly in a Texas court on Tuesday as the jury's decision, which only took 30 minutes, was read.
He would be eligible for parole in 35 years, said the Texas Department of Criminal Justice.
Jeffs had referred to himself as a prophet, and the Mormon breakaway sect he leads believes polygamy is the path to heaven.
During the trial, prosecutors presented DNA evidence to show Jeffs had fathered a child with a 15-year-old girl, and an audio recording of him sexually assaulting a 12-year-old.
The jury heard other tapes in which Jeffs was heard instructing his young wives on how to satisfy him sexually, which he said would please God.
Jeffs, who insisted on acting as his own legal defence during the earlier part of the trial, argued he had been prosecuted because of his religious beliefs.
The sect leader refused to speak during the sentencing portion of the trial, with a defence lawyer telling the judge his client had instructed his legal team not to speak for him.
Jeffs, who had stood expressionless and silent before the jury for nearly half hour during his closing arguments, called only one defence witness to the stand - a man who read from Mormon scripture.
Prosecutors said the religious head had spent years travelling around North America and avoiding arrest, ultimately landing on the FBI's 10 Most Wanted list.
An FBI agent said during the trial that fathers who handed over their daughters to Jeffs were rewarded with young brides of their own.
"If the world knew what I was doing, they would hang me from the highest tree," Jeffs wrote in notes, seized from his Texas ranch.
When police raided the Texas ranch they found women dressed in frontier-style dresses and underage girls who were clearly pregnant.
The 10,000-strong sect, which dominates the towns of Colorado City in Arizona, and Hildale, Utah, split from the mainstream Mormon church more than a century ago.
Polygamist sect leader Warren Jeffs has been sentenced to life in prison for sexually assaulting two underage followers he took as brides.