Buffett put his money behind his long-held argument that "experts" don't do better than the stock market as a whole. It's the basis of his argument that the fees "helpers" charge investors usually aren't justified.
In a Fortune piece, long-time Buffett friend Carol Loomis writes that after six years the fund Buffett selected for the wager, the Vanguard 500 Index Fund Admiral Shares, was up 43.8 percent at the end of 2013.
(Read more: Read a 10-K like Warren Buffett)
The other side of the bet is a collection of five hedge funds of funds chosen by New York-based Protégé Partners.
After all fees, their average gain was about 12.5 percent. The names of the funds have not been revealed.
After trailing for the first four years, Buffett's choice pulled ahead at the bet's halfway mark, with a gain of 8.69 percent vs. 0.13 percent for the hedge funds as of the end of 2012.
(Read more: Is Warren Buffetttoo big to fail?)
Now that Buffett has increased that lead, Protégé's Ted Seides said in the Fortune piece, "We've got our work cut out for us."
The prize, Berkshire Hathaway stock worth almost $1.3 million as of the end of 2013, will go to the winner's chosen charity. Buffett designated Girls Inc. of Omaha ("Inspiring all girls to be strong, smart, and bold") while Protégé chose U.K.-based Absolute Returns for Kids ("An international organization whose purpose is to transform children's lives.")
Originally the pot consisted of zero-coupon bonds that would be worth $1 million when the contest ended. Due to low interest rates, however, the value of the bonds came close to the target by the end of 2012. The two sides agreed to sell the bonds and buy Berkshire stock with the proceeds.
That turned out to be a good decision, as shares of Buffett's company soared more than 32 percent last year.
—By CNBC's Alex Crippen. Follow him on Twitter: @alexcrippen