Hernandez's body was found Sunday from California's aqueduct, Sheriff Margaret Mims said at a news conference.
Her body was discovered weighed down beneath the surface, Mims said, giving no further details.
The delicate diving operation took about three hours as divers searched in the cold water. Each diver could only go below the surface for about 30 minutes at a time and could not touch the bottom of the aqueduct as the disturbance of silt on the bottom obscured the visibility, Mims explained.
"While today's announcement is both sad and meaningful to Missy's family and her loved ones, it will not change the charges in the case," Jerry Stanley, assistant prosecutor in Fresno County, said Tuesday. "However, it adds a critical new component of evidence to the case that will help our pursuit of justice for Missy and her family."
Fresno County District Attorney Lisa Smittcamp said last week that Jimenez had appeared in court with a public defender and that his next hearing was scheduled for March 22, after which a lawyer would be officially appointed for his case. The Fresno County Public Defender's Office declined to comment Friday.
Hernandez, 30, was last seen at an art show in downtown Fresno on Dec. 7 with Jimenez, authorities said earlier.
Her friends contacted authorities the next day after they could not reach her, and a deputy responded to her home and did not find her, but contacted Jimenez, authorities said. The deputy investigated the home's address and recognized Jimenez as a suspect wanted for an incident of domestic violence against Hernandez at the same address in October, the sheriff told reporters last week.
Since Jimenez was arrested last month, investigators have gathered "an overwhelming amount of forensic and digital evidence," Mims said, including "DNA indicating that a violent act took place in Missy's home."
Jimenez risks a 25-year sentence to life in prison if convicted, Smittcamp told reporters last week.
CNN's Dakin Andone contributed to this report..