Bardem accepted for the absent Coens, saying, "I'm the third brother, the Spanish one."
Awards came in pairs for three other films: "Hairspray," "Juno" and "There Will Be Blood."
The cast of "Hairspray" was named best acting ensemble and its breakout star, Nikki Blonsky, won best young actress.
The 19-year-old thanked "my mommy who's sitting here crying and my other mommy who's at home, John Travolta." Travolta famously cross-dressed to play Edna Turnblad.
The teen-pregnancy film "Juno" collected trophies for best comedy and for screenwriter Diablo Cody.
"There Will Be Blood" earned the best actor honor for star Daniel Day-Lewis, and composer Jonny Greenwood won best composer for his haunting score of the film.
The Writers Guild of America strike, which began Nov. 5, has effectively shut down Hollywood and cast a pall over Tinseltown's awards season. But the Critics' Choice Awards, presented by the Broadcast Film Critics Association at the Santa Monica Civic Auditorium and broadcast live on VH1, wasn't covered by guild contracts.
Julie Christie won best actress for "Away From Her," but she wasn't on hand to accept her prize. Also absent was best young actor Ahmad Khan Mahmoodzada, star of "The Kite Runner," and supporting actress Amy Ryan, who co-starred opposite Casey Affleck in "Gone Baby Gone."
Glen Hansard and Marketa Irglova, who won best song for their work in "Once," also skipped the ceremony.
"I look at it as a win for all the people who worked on the film. It was a film that was long in gestation," he said. "Animation is coming more and more to the forefront and it's great because people see that it's not an obscure art form, it's something accessible and fun."
"Enchanted" won best family film, "Bury My Heart at Wounded Knee" was best made-for-TV movie and "Sicko" was best documentary feature.
The critics chose "The Diving Bell and the Butterfly" as the best foreign film. Director Julian Schnabel was humbled by his win. Asked backstage how he felt, Schnabel said, "a little drunk and pleasantly surprised."
Before introducing his friend, Clooney noted the impact of the Hollywood writers' strike on the city.
"This is a one-industry town and when a strike happens it's not just writers or actors, it's restaurants and hotels and agencies," he said. "And our hope is that all of the players involved will lock themselves in a room and not come out until they finish."
Cheadle also acknowledged the strike, saying it kept him from writing an acceptance speech.
The Broadcast Film Critics Association, which represents more than 200 TV, radio and online critics from the United States and Canada, founded the Critics' Choice Awards in 1995.
"Into the Wild," written and directed by Sean Penn, had a leading seven nominations but didn't win any.
On the Net: