Duchamp sent the original urinal to a New York show in 1917
The set of the French artist's found and altered objects, which also included a bicycle wheel attached to a kitchen stool, fetched $5.3m (£3.7m) in total, with two lots failing to sell at all.
The urinal, titled The Fountain, sold for $1,185,000 (£816,000), short of its low estimate of $1.5m, at the Phillips de Pury & Luxembourg auction.
But work by more contemporary artists, including Francis Bacon, Jeff Koons and minimalist sculptor Donald Judd sold for high prices.
The evening's top lot was Bacon's Study For Portrait Of Henrietta Moraes, which sold for $6,712,500 (£4,625,000) - close to the high estimate of $7m and one of the highest prices ever paid for a Bacon.
A Donald Judd sculpture in galvanized steel from 1967, Untitled, also attracted very competitive bidding, eventually selling for $1,322,500 (£911,000), nearly double its high estimate.
The price broke the record for a Judd sale, previously $819,750.
Canvas
The record also fell for pop artist Edward Ruscha, whose 1963 work Untitled (Noise), went for an unexpected $2,532,500 (£1,745,000) or nearly four times the old record of $687,750.
The work is a large canvas in blue with the word "noise" painted in large yellow block letters and had been estimated at $1m to $1.5m.
Jeff Koons' sculpture Aqualung sold for $1,762,500 (£1,215,000), in the range of its pre-sale estimates.
The total raised by the sale was $29,686,350 (£20,460,000), just beating the low estimate of $28.5m.
Michael McGinnis, director of contemporary art for the auction house, said that the market for Duchamp's work was "very much untested".
"It was very difficult for the market to identify what the estimates were."
But Mr McGinnis said the auctioneers were "very happy" with the performance of the other lots which, he said, reflected "a very strong market, with a lot of buyers".
And referring to last year's attacks on the US, he added: "Post 9-11 there seems to be an incredible resilience for paintings that evoke a lighter side of life."