Details of the agreement were not disclosed at the brief court hearing, but the judge said he felt that settlement talks had led to resolution.
The divorce will become final once papers are prepared and signed by the parties.
Kim appeared with her lawyer and said she understood the terms of the agreement.
Kris did not attend. The judge dropped an order for the NBA player to appear and explain why he failed to attend a previous hearing.
Kim and Kris were married in August 2011. She filed for divorce after 72 days of marriage.
Kris had wanted the marriage annulled based on his claims that it was fraudulent, because of his belief that she only married him because of her reality show 'Keeping Up With The Kardashians'.
Kim denied the accusation.
The reality TV star is expecting her first child with rapper Kanye West this summer.