The Jack Russell beat competition from other dogs that appeared in Hugo, Beginners, 50/50 and Young Adult.
Trainer Omar Von Muller accepted the award with Uggie, whose performance in Water For Elephants also made the shortlist, at the Los Angeles ceremony.
The inaugural awards recognise canine excellence in Hollywood on both the big and small screens.
Von Muller said the award was "overwhelming" adding: "He has been my buddy forever and is a great performer and great family member."
He also thanked award organisers DogNewsDaily.com saying: "This is very important for all the trainers in the movie industry, because we have never been recognised before, and people just don't understand that it takes hundreds and even thousands of hours to train a dog."
Ten-year-old Uggie has had a long career in film and television and retired following The Artist, for which he was also awarded the Palm Dog at the Cannes Film Festival.
The ceremony saw prizes awarded in five other categories, including best dog in a foreign film, best dog in a television series, best dog in a reality series and best dog in a direct-to-DVD film.
A special prize was also awarded to actress Charlize Theron - who was not present at the event - for her work on behalf of animal welfare.
Martin Scorsese also appeared at the ceremony by video.
The Hugo director wrote an editorial in the Los Angeles Times last month urging readers to begin a write-in campaign to recognise Blackie the Doberman, who starred in his film, in the main film category.
Although Blackie lost out to Uggie, the director thanked fans for their support and joked: "I remain shocked by the suggestion that Blackie was in any way augmented or enhanced by CGI and I can only hope this innuendo in no way affected the voting."
Other winners included French bulldog Brigitte, who plays Stella on US sitcom Modern Family, and Hercules of Animal Planet show Pit Boss who tied with Giggy of The Real Housewives of Beverly Hills for best dog in a reality television series.
The ceremony was broadcast online by the Hollywood Reporter, and Alan Siskind from DogDailyNews said he expected the ceremony to be televised next year.
Uggie, the canine star of The Artist, has been named best dog in a theatrical film at the Golden Collar awards.