The winning bid was made just six minutes before the online auction ended at 10:30 p.m. ET Friday night.
Read More Why Buffett, Apple and Google love the Mojave Desert
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.
Read More Two stocks costing Buffett $500M this 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: