Details of the agreement were not disclosed in a brief court hearing Friday, 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.
Kardashian appeared with her lawyer and said she understood the terms of the agreement.
Humphries did not attend. The judge dropped an order for the NBA player to appear and explain why he failed to attend a previous hearing.
Kardashian and Humphries were married in August 2011. She filed for divorce later that year.