The Moi Teaching and Referral Hospital in Eldoret city confirmed Cheptegei's death on Thursday.
A spokesperson said the long-distance runner, 33, died early in the morning after her organs failed.
She had been fully sedated on admission at the hospital.
Cheptegei competed in the women's marathon at the Paris Olympics less than a month before the attack.
She finished in 44th place.
Her father, Joseph Cheptegei, told journalists at the hospital he had lost a daughter who was "very supportive" and he hoped to get justice.
On behalf of — TeamKenya (@OlympicsKe) #TeamKenya we extend our deepest condolences to the Ugandan sports community, family, and friends of Rebecca Cheptegei. Rebecca's talent, and perseverance as Uganda's Women's Marathon record holder and a Paris 2024 Olympian will always be remembered and celebrated.… pic.twitter.com/k3hNYB9WOPSeptember 5, 2024
Trans Nzoia County Police Commander Jeremiah ole Kosiom said Cheptegei's partner, Dickson Ndiema, bought a can of petrol, poured it on her and set her ablaze during a disagreement on Sunday.
Ndiema was also burned and was being treated at the same hospital.
Menach said Ndiema was still in the intensive care unit with burns over 30 per cent of his body but was "improving and stable".
Cheptegei's parents said their daughter bought land in Trans Nzoia to be near the county's many athletic training centres.
A report filed by the local chief said the two were heard fighting over the land where her house was built before the attack.
The Uganda Athletics Federation eulogised Cheptegei on the social platform X, writing: "We are deeply saddened to announce the passing of our athlete, Rebecca Cheptegei, early this morning who tragically fell victim to domestic violence.
"As a federation, we condemn such acts and call for justice. May her soul rest in peace."
Uganda Olympic Committee president Donald Rukare called the attack "a cowardly and senseless act that has led to the loss of a great athlete".
In 2023, Ugandan Olympic runner and steeplechaser Benjamin Kiplagat was found dead with stab wounds.
In 2022, Kenyan-born Bahraini athlete Damaris Muthee was found dead and an autopsy report said she was strangled.
In 2021, long distance runner Agnes Tirop was stabbed to death at her home.
Her husband, Ibrahim Rotich, was arrested and charged with murder, the case is ongoing.
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