A representative of the San Francisco-based Glide Foundation, which gets 100 percent of the profits from the sale, identified the winner as Andy Chua of EMES in Singapore.
The winning bid was made just six minutes before the online auction ended at 10:30 p.m. ET Friday night.
This year's price is more than double the $1,001,000 paid by last year's anonymous winning bidder.
In 2012, an anonymous bidder paid a record $3,456,789 for a meal with Buffett.
Ted Weschler, now a portfolio manager at Berkshire Hathaway, won both the 2010 and 2011 auctions, paying more than $2.6 million each year.
Glide has received more than $16 million from Buffett lunch auctions over the past 15 years.
Glide's co-founder and Minister of Liberation, Reverend Cecil Williams, is quoted as saying, "Our true mission at Glide has always been to serve the poor first and foremost and Mr. Buffett's generosity helps us do that in a powerfully human way."
The winner, and up to seven others, will have the opportunity to share a lunch with Buffett at New York City's Smith & Wollensky steakhouse. Some winners, however, have preferred to meet with Buffett in his home town of Omaha.
Here's a look at the price of lunch with Buffett over the years:
-By CNBC's Alex Crippen. Follow him on Twitter: @alexcrippen