The 74-year-old motor racing star collected the award from Edinburgh Napier University at a ceremony in the city.
Known as the Flying Scot, he won 27 grands prix and was Formula One world champion three times.
Sir Jackie said: "I am very proud to have been selected for an honorary degree at Edinburgh Napier University. It is always nice to be recognised, particularly in your own country."
Since the end of his career, Sir Jackie has acted as a commentator and racing safety advocate. He is also president of the charity Dyslexia Scotland after discovering he had the condition at the age of 42.
The former champion, from West Dunbartonshire, who received a knighthood in 2001, has previously told how his dyslexia went undiagnosed throughout his time at school. He said he believes it pushed him to find success in other areas, including in racing and business.
He joined almost 1,000 students for the graduation ceremony at Edinburgh's Usher Hall.