Including commission, the unidentified telephone bidder paid nearly $12.4 million for the gem, putting the price within the $11 million to $15 million range Sotheby's had estimated before the sale.
The head of Sotheby's jewelry division said it was the eighth most expensive diamond ever sold at auction.
The pear-shaped Sun-Drop Diamond beat previous records for a jewel of its type.
The 110.3-carat diamond was found in South Africa last year and has the highest possible color grading. Gemologists had rated it as fancy, vivid yellow.
Yellow diamonds are created by nitrogen impurities being trapped within carbon molecules and hardening over the course of millions of years.
The Associated Press contributed to this report.