Green, who has five wives and 33 children as part of the polygamist lifestyle he espoused, cried and expressed remorse for his marriage to Linda Kunz Green, who is now 30.
The sentence by Juab County District Judge Donald Eyre was the lightest he could have given Green. A parole board will determine when Green, who is serving a five-year term for being married to five women simultaneously, will be released.
Defense attorney John Bucher said his client never imagined the consequences of his lifestyle could be so harsh.
"It's all hit him like a ton of bricks," said Bucher, who plans to appeal. "He's very depressed about it."
Bucher believes Green could be released from prison in less than four years.
"I couldn't be any more sorry for marrying Linda when I did," Green said before the sentence was handed down. "I accept full responsibility. I never have blamed my victim."
Green also told the court that "I recognize, under the law, she was not capable of consenting to marriage."
Eyre said he was giving Green a lesser sentence in part because Linda Kunz Green has remained devoted to him.
"We should do everything possible to protect children," he said. "Clearly there is a pattern with children, involvement with young girls, and that's an aggravating circumstance."
On the other hand, he said: "Linda Green is his strongest supporter and she's maintained her devotion to him."
Linda Kunz Green said she does not consider herself a victim and told the judge that he should consider the children who would be without a father while their father was in prison.
"I'm not a 13-year-old girl, I'm a 30-year-old woman who has seven children and is capable and independent," she said. "I do not consider myself a victim of Thomas Green. It was me who fell in love with him," she said.
Kunz Green - who was Green's stepdaughter before their marriage - also says she's the one who initiated the relationship and was the pursuer.
Prosecutor Monte Stewart had asked the judge to sentence Green to 10 years to life in prison, saying that Linda Kunz Green's support could not lessen the seriousness of the crime.
"A 37-year-old man having sexual intercourse with a 13-year-old girl is never justified," he said. "He knew it was against the law and he went ahead and did it. I have seen nothing that suggests that Tom Green has any genuine remorse."
Another prosecutor in the case, David Leavitt - a brother of Utah Gov. Mike Leavitt - compared Linda Kunz Green's love for her husband as being similar to the affinity hostages sometimes feel for their captors.
"People in the state of Utah simply do not understand the devastating impact of polygamy on young girls," said Leavitt, arguing for a maximum sentence.
Green has admitted having sexual intercourse with Linda Kunz after he married her in 1986 when he was 37 and she was just 13. But he argued at trial that the marriage took place in Mexico and that Utah authorities had no jurisdiction.
The defense also said the statute of limitations had run out on the crime, but the judge had previously ruled that the statute did not begin to run until authorities saw Green on television talking about his polygamous life. Green has said officials knew about his living arrangements for years, but did nothing until he appeared on TV.
Anti-polygamy groups say many people in rural Utah practice plural marriage, believing it adheres to the original guidance of the Church of Jesus Christ of Latter-day Saints - more commonly called the Mormon Church. Green holds such beliefs.
The church banned the practice in 1890 to win full statehood in the United States for Utah, where it is the predominant religion.