The actor is also nominated in the director and original screenplay categories for Good Night, and Good Luck, at the Academy Awards on Sunday.
Clooney's first Oscar win cemented his journey from the man once dubbed the "sexiest man alive" by People magazine to a leading Hollywood heavyweight with a passion for making films on risky subjects.
He is also one of Hollywood's best-known liberals and an actor who has no qualms about wearing his political heart on his sleeve.
Clooney, who had never even attended the Academy Awards until this year, is the only person in Oscars history to be nominated for acting in one movie and directing another in the same year.
In a highly political Oscars year featuring a clutch of films that tackle real-world problems, the actor says his films raise important questions.
"It's your right or duty to question and ask questions. I don't think we provide any answers; we just ask a lot of questions," said Clooney, one of Hollywood's most liberal stars who has frequently criticised the Bush administration.
In Stephen Gaghan's complex thriller Syriana, about the oil industry in the Middle East and the US government's murky involvement in it, Clooney plays weary veteran CIA agent Bob Barnes.
He gained more than 13kg to look the part of a haggard man and injured his spine while filming a scene in which his character is tortured, needing several operations.
The black-and-white Good Night, and Good Luck, which Clooney also co-wrote and co-stars in, tells the story of newsman Edward Murrow's battle against the repression of the 1950s communist witch hunt in the United States.
Best actress - Reese Witherspoon, Walk the line
Best lead actor - Philip Seymour Hoffman, Capote
Lifetime achievement award - Robert Altman
Foreign-language film - Tsotsi (South Africa)
Visual Effects - King Kong
Animated feature - Wallace & Gromit in the Curse of the Were-Rabbit
Live Action Short Film - Six Shooter
Animated Short Film - The Moon and the Son: An Imagined Conversation
Costume Design - Memoirs of a Geisha
Makeup - The Chronicles of Narnia: The Lion, the Witch, and the Wardrobe
Supporting Actress - Rachel Weisz, The Constant Gardener
Documentary Short - A Note of Triumph: The Golden Age of Norman Corwin
Documentary Feature - March of the Penguins