The sale of the 13.22-carat rock known simply as "The Blue" came a day after Sotheby's sold a 110-carat flawless yellow diamond for $16.3 million -- with both sales including commission.
When the world's largest orange diamond went under the hammer last November at Christie's in Geneva, it raked in $35.5 million.
Such marquee sales underline the growing popularity of coloured diamonds.
Once considered a curiosity, they are rarer than white diamonds and now attract higher prices per carat than even the most flawless, translucent stone.
The US jeweller Harry Winston bought the blue diamond, described by Christie's as the largest fancy vivid blue diamond in the world, from an anonymous seller.
"Fancy vivid" is the top rating for coloured diamonds.
The company's CEO Nayla Hayek said it plans to rename the 13.22-carat pear-shaped rock the "Winston Blue".
Harry Winston was bought by Swiss-based watch group Swatch last year.
“In January 2013 we purchased Harry Winston and since then my ambition has been to acquire the most desirable and unique gems," Hayek said in a statement.
"When Christie’s announced they were offering the largest flawless fancy-vivid blue the GIA (Gemological Institute of America) had ever graded, I had to buy it."
The sale was part of the "Geneva Magnificent Jewels" auction that raked in 139 million francs, including buyer's commissions.