Chief Justice Martha Koome on Saturday visited the home of Makadara Principal Magistrate Monica Kivuti.
Kivuti was shot on Thursday afternoon at the Makadara Law Courts after she made a ruling in a case involving a policeman's wife.
Koome said on Saturday she succumbed to the injuries she sustained from the shooting incident.
The CJ condoled with the family who were coming to terms with Kivuti's untimely death.
The Chief Justice signed the condolence book placed at the entrance of the deceased Judicial officer's house.
Earlier while confirming Kivuti's death, CJ Koome said the Judiciary stands with her family and friends.
"We condole with the family, friends and the entire Judiciary fraternity during this very difficult period of mourning. The Judiciary family stands in solidarity during this deeply traumatic time and calls for sensitivity and compassion as we share in grief," she said.
Kivuti died at the Nairobi Hospital on Friday where she was transferred for specialised care after the shooting incident.
She was shot and injured in the hip area and on the chest.
Kivuti was rushed to Metropolitan Hospital and later transferred to Nairobi Hospital.
On Friday, an urgent blood appeal was made to help save her life but she succumbed to her injuries later that night at around 11pm.
"Urgent appeal for blood donation. This is to kindly request blood donation for Hon Monica Kivuti," Law Society of Kenya (LSK) male representative at the Judicial Service Commission (JSC) Omwanza Ombati said.
Her family said the body was moved to Lee Funeral Home.
In a statement on Thursday, Koome said the magistrate was shot after she "cancelled the bond for an accused person who had jumped bond and had failed to offer satisfactory explanations for jumping bond".
"Immediately this decision was pronounced, a person shot at the magistrate and injured her on the hip,” she said.
The officer, identified as Chief Inspector Samson Kipchirchir Kipruto, who was in charge of a police station in Londiani in Kisumu, pulled out a gun and shot the magistrate, injuring her.
Other officers in court responded immediately, with one of them shooting the offending policeman and killing him on the spot.
Three other officers were injured in the ensuing melee, police said in their report.