Sotheby's says "Pink Panther" had been estimated to bring $20 million to $30 million.
There were three editions made of the work; the one at Tuesday's auction is the artist's proof.
One was sold at Christie's in 1999 for $1.8 million, reportedly to the newsprint magnate Peter Brant. The others are in the Museum of Modern Art and the Museum of Contemporary Art in Chicago.
Sotheby's didn't disclose the seller's name.
Koons' "Balloon Flower Magenta" sold for $25.7 million in 2008 at Christie's. It set a record for the artist.