"I think this is a reasonable way to resolve this case," said Superior Court Judge Hank Goldberg, who did not disclose terms of the settlement.
Humphries sent his lawyer but did not appear in court. Kardashian, who is pregnant with a child by her boyfriend Kanye West, appeared in a black silk puffy sleeveless maternity dress embellished with sequins on the skirt.
"Ms. Kardashian, is this your signature?" the judge asked her as he perused a three-page settlement agreement.
"Yes," she replied. She continued to answer yes when asked if she had discussed the matter with her attorney and understood that there would be no trial.
"During your marriage did irreconcilable differences occur?" the judge asked.
"Yes," said Kardashian.
"Is there any way your marriage can be saved?" he asked.
"No," said Kardashian.
She married the NBA player in a high-profile wedding in August 2011. She filed for divorce later that year.
He sought an annulment claiming their marriage in an elaborate wedding ceremony was a fraud staged for her reality show, "Keeping Up With the Kardashians."
She denied the allegations and insisted on a traditional divorce. She apparently won.
"The court is going to grant dissolution of marriage," the judge said, advising that the divorce would not be final until papers are drawn up and signed.
Humphries did not attend the brief hearing. His lawyer, Benjamin Johnson, said he agreed to the settlement. The judge dropped an order for the Brooklyn Nets power forward to appear and explain why he failed to attend a previous hearing.
Kardashian was hustled into court by sheriff's deputies through a back entrance and no photos were allowed.
The judge congratulated Johnson and Kardashian's attorney, Laura Wasser, for achieving the settlement.
"I wish both parties the best of luck as they move forward with their lives," he said.