The text is believed to be one of about 15 surviving copies of an oversize printing of the proclamation made by a pair of Philadelphians in 1864 to raise money for war relief. The Emancipation Proclamation, freeing the slaves in the Confederate states, was issued in 1863.
Christie's auction house declined to identify the buyer but said it was a New York-based dealer.
The document was one of a number of remarkable items on the auction block Tuesday from Forbes' collection of American historical documents.
Letters from or about Lincoln dominated the list of top sellers.
One buyer paid $307,100 for the first printing of the Gettysburg Address, dating from 1863. A report from the president's doctor, detailing his death and autopsy, sold for $240,000.
A few Civil War documents offered for sale failed to attract buyers, including Julia Ward Howe's original draft of "The Battle Hymn of the Republic" and a letter that Robert E. Lee wrote to his son lamenting the death of Lt. Gen. T.J. "Stonewall" Jackson.
From a more recent period, the collection contained a map of Japan carried by the crew of the Enola Gay on its mission to bomb Hiroshima. It sold for $72,000.
A buyer paid $42,000 for two pages from the speech that Theodore Roosevelt carried in his vest pocket the night he survived an assassination attempt in 1912.
A bullet pierced the manuscript and a metal spectacle case but didn't seriously harm Roosevelt, who continued on to an auditorium to address the waiting crowd.
Holding up the perforated speech for all to see, Roosevelt exclaimed, "It takes more than that to kill a Bull Moose."
In all, the auction took in $5.2 million, in line with presale estimates, a Christie's spokeswoman said.
The prices included a house premium of 20 percent on the first $200,000 and 12 percent thereafter.
For several years the Forbes family has been selling parts of the collection. Another batch of items is scheduled for sale next year.