Horse, which each got six nods for the Academy Awards, to be presented next month.
Meryl Streep, as expected, received her 17th Oscar nomination for a gripping performance as former British premier Margaret Thatcher in The Iron Lady, while those shortlisted for best actor included Pitt and George Clooney.
Foreign language nominees included Iran's powerful drama A Separation, which won the Golden Globe in that category earlier this month, along with films from Israel, Belgium, Poland and Canada.
Hugo's nominations included the best picture category, where it is up against eight other movies including The Artist, which has been a favorite for the Oscars after a string of wins and nods in other awards show.
The Scorsese movie -- his debut in 3D -- is a visually rich tale set in 1930s Paris, about an orphan who lives in the walls of a train station and is obsessed with clock-making and early film pioneer Georges Melies.
The film stars British teenage actor Asa Butterfield in the title role with Ben Kingsley as Melies and British "Borat" and "Bruno" star Sacha Baron Cohen as the lugubrious station inspector.
Scorsese said he was "deeply honored" by the nominations, and joked about the challenges he faced in making Hugo.
"Every picture is a challenge, and this one -- where I was working with 3D, HD and Sacha Baron Cohen for the first time -- was no exception," he said, teasing the flamboyant actor who acts with understated comedy in the movie.
"Its a wonderful feeling to know that youve been recognized by the people in your industry. I congratulate my fellow nominees. Its an impressive list, and Im in excellent company," he told the Hollywood Reporter.
"The Artist" has already been nominated for best film by the Directors Guild of America (DGA) and won the top prize from the Producers Guild of America (PGA) last week -- both seen as key indicators of Oscars glory.
The film, a tribute to the silent movie era in which a non-talking star battles to save his career after it is torpedoed by the arrival of the "talkies," also won the best picture Golden Globe on January 15.
The other movies nominated for best picture are The Descendants, Extremely Loud and Incredibly Close, The Help, Midnight in Paris, Moneyball, The Tree of Life and War Horse.
The Artist star Jean Dujardin was nominated for best actor, up against Clooney in The Descendants, Pitt in Moneyball, Gary Oldman in Tinker Tailor Soldier Spy and Demian Bechir in A Better Life.
Two-time Oscar winner Streep is among best actress nominees for the latest tour de force in her long career, playing Thatcher both in her prime and dementia-shrouded old age.
Also shortlisted were Glenn Close for cross-dressing Albert Nobbs, Viola Davis from civil rights drama The Help, Michelle Williams as Monroe in My Week with Marilyn and Rooney Mara from The Girl with the Dragon Tattoo.
Up for best foreign language film are A Separation by Iranian filmmaker Asghar Farhadi, along with Footnote (Israel), In Darkness (Poland), Monsieur Lazhar (Canada), and Bullhead (Belgium).
The Oscars are to be presented at the Kodak Theatre in Hollyood on Sunday, February 26.