"Her Majesty The Queen has announced that South African Olympic and Paralympic medal-winning swimmer Natalie du Toit has been awarded an honorary MBE for her services to Paralympic sport," the commission said in a statement.
Du Toit said upon hearing of the award: "I find myself extremely humbled and honoured to be receiving this auspicious award. To those that have made it possible I thank you for believing in me and by having stayed by my side."
British acting High Commissioner Martin Reynolds said: "Natalie has achieved great success in her sport, demonstrating an ability to compete with the best in both Olympic and Paralympic disciplines at numerous international sporting events.
"Natalie is an inspiration to up and coming athletes throughout the world and I am delighted she has been recognised for her achievements."
The United Kingdom was proud to have helped shape Du Toit's career, with her first competition being the 2002 Commonwealth Games in Manchester, said Reynolds.
Du Toit retired after the 2012 London Olympic and Paralympic Games, where she won three gold and one silver medal.
"She has been an inspiration for a generation of Paralympians and we are delighted that her contribution has been recognised," he said.
Du Toit would be presented with the award at a ceremony by His Royal Highness The Earl of Wessex in October in Pretoria.