The egg-shaped stone has been described as the finest of its kind ever to appear at auction. Earlier estimates valued it at $28-$35 million.
The stone, dubbed the "Magnificent Oval Diamond", was discovered in a deep mine in an undisclosed southern African country in 2011.
As a rough stone before being cut, it weighed 299 carats.
The stone, described by Sotheby's as "the largest D colour flawless diamond", has been given the highest quality rating awarded by the Gemological Institute of America.
"D colour" diamonds are rare and colourless and fetch premium prices.
The sale beat the record set at a diamond auction last year, when a 101.73-carat diamond was sold for $26.7 million.
Hong Kong has become a centre for jewellery auctions thanks to growing wealth in China and other parts of the region.