The most prized item of the 350 offered by Brando's estate was his annotated script for the 1972 classic film, which earned him an Oscar for his portrayal of Don Corleone.
The item fetched $312,800 — a record price for a film script.
The previous top seller, Clark Gable's "Gone with the Wind (search)" script, sold for $244,500 at Christie's in 1996.
The Brando script, which had been valued at just $10,000-$15,000, was won by an anonymous phone bidder after a furious flurry of offers.
Another highlight of the 61/2-hour sale before a packed room of 500 was a letter from "Godfather" novel author Mario Puzo, asking Brando to consider starring in the movie. It went for $132,000.
Other highlights included a steamy photo of the star, sporting blond hair and holding a nude actress from a 1968 movie love scene. It earned $48,000.
And a transcript of a telegram from Brando to Marilyn Monroe after her nervous breakdown in 1961 took $36,000.
Marilyn Gauthier, who runs a modeling agency, shelled out $11,000 for a set of the superstar's bongo.
"Brando has always been my idol. He was the best actor of the 20th century and he's gorgeous, too. He had everything," she gushed.