The stars were handed the gongs for 'Best Actress' and 'Best Actor' at the 46th edition of the annual event.
Dunst was honoured for her role in Lars von Trier's Melancholia, which also earned 'Best Picture'. She got the nod head of Yun Jung-hee for her role in Poetry and Meryl Streep in The Iron Lady.
Pitt earned his prize for Moneyball and The Tree of Life. The latter missed out on 'Best Picture' to von Trier's apocalyptic drama, but landed Terrence Malick the 'Best Director' honour and helped Jessica Chastain earn 'Best Supporting Actress'.
Albert Brooks also bagged a 'Best Supporting Actor' gong for his role in Drive.
The National Society of Film Critics is made up of 58 of the most prominent movie critics in the US. It held its 46th annual awards voting meeting at Sardi's Restaurant in New York City.
List of winners in full:
Best Picture: Melancholia
Best Director: Terrence Malick, The Tree of Life
Best Actor: Brad Pitt, Moneyball, The Tree of Life
Best Actress: Kirsten Dunst, Melancholia
Best Supporting Actor: Albert Brooks, Drive
Best Supporting Actress: Jessica Chastain, The Tree of Life, Take Shelter, The Help
Best Screenplay: A Separation, Asghar Farhadi
Best Cinematography: The Tree of Life, Emmanuel Lubezki
Best Nonfiction Film: Cave of Forgotten Dreams, Werner Herzog
Best Foreign Language Film: A Separation, Asghar Farhadi
Best Experimental Film: Seeking the Monkey King, Ken Jacobs
Watch a trailer for Melancholia below: