Larry Roth, a philanthropist based on Long Island, bought the car at the Formula One Grand Prix in Austin, Texas over the weekend. (Read more: For Now, Rich Sit on Wallets in Sandy's Wake)
The F12 is the most powerful production Ferrari ever sold, with a V12 engine that helps the car reach a top speed of 211 mph.
Combined with contributions from dealers, clients and "friends" of Ferrari, the sale of the Berlinetta put the amount Ferrari, a division of Fiat, has raised for Sandy charities at more than $1.5 million. (Read more: Charity Gets Nine Percent of Millionaires' Income)
Roth, who lives in Great Neck, N.Y., made his fortune from starting an eye-glasses business, which he sold in 2008. He said that he already owns two Ferraris – a 599 GTO and a 2013 458 Spyder he received a month ago.
He said he didn't plan on getting another Ferrari, but had already planned to attend the Formula One race in Texas. When he found out that the Ferrari sale was benefitting Sandy victims, he felt he had to bid.
"I had no intentions of purchasing another Ferrari," he said. "But I had so many friends and people I knew who were impacted, I thought this was a great way to help."
He said that he originally planned to bid no more than $1 million, "but when I got in the auction, my wife and I decided we would bid whatever it took to win."
Roth gets an added benefit with his gift. While other buyers of the F12 Berlinetta will have to wait two years for their cars, Roth will get his in the second quarter of 2013.
-By CNBC's Robert Frank
Follow Robert Frank on Twitter: @robtfrank