The copy, one of only five originals of the thesis entitled "Properties of expanding universes", smashed pre-sale expectations four times over to sell for £584,750 at the Christie's sale, which ended on Thursday.
A red leather wheelchair that Hawking used from the late 1980s to the mid-1990s, driving himself using a joystick, sold for £296,750 while an early edition of his bestselling book "A Brief History of Time" marked with a thumbprint, fetched £68,750.
A script from one of his appearances on the television series "The Simpsons" was one of the 22 lots under the hammer, selling for £6,250.
The collection highlighted the brilliance, determination and sense of humour of Hawking, who died in March aged 76 after a lifetime spent trying to unlock the secrets of the universe.
Hawking published his thesis in 1965, two years after being diagnosed with amyotrophic lateral sclerosis (ALS), a form of motor-neurone disease that would eventually leave him paralysed.
His first wife Jane typed out the 117 pages but he added two hand-written signatures and the words "This dissertation is my original work" at the front, as well as several mathematical equations inside.
When the document was made available online last year by Cambridge University, where Hawking spent his career, it was so popular that it crashed the website.