The 33-year-old Sheffield-born Team GB ambassador travelled on a specialist medical plane with a team of professionals who continued her care on the 20-hour journey.
Webster’s condition remains stable but serious, and she will continue her treatment in a private ward at St James’s Hospital in Leeds.
In a message dictated from her hospital bed, she said: “I’m so grateful to the staff at Copa D’or hospital in Rio for the care I received, they saved my life.
“The last few weeks have been hell and I’m just so thankful to be here.
“I have the most wonderful family and friends supporting me and the well wishes from the public has been incredible. I’m happy to be home to continue my recovery in the UK.”
Webster fell ill during the opening ceremony of the Rio Olympics and she was taken to hospital on August 6.
The former Sky and ITV sports presenter had just completed a 3,000-mile (4,828km) charity cycle ride from London to Rio.
Her condition quickly deteriorated and she was put into a medically induced coma. Doctors diagnosed a very rare strain of malaria and medical specialists are now trying to find out where she may have caught the disease.
Last week, Webster was able to get out of bed for the first time and her kidney dialysis was reduced to six hours a day.