The win would normally be an indicator of Oscar success as the Directors Guild recipient nearly always goes on to claim the same prize at Hollywood's biggest night.
But Affleck missed out on an Oscar directing nomination.
"I don't think that this makes me a real director, but I think it means I'm on my way," said Affleck of the win.
In Argo, set amidst the 1979 Iranian hostage crisis, Affleck also plays the lead role of a CIA agent entrusted with extracting six Americans from the country after the US embassy was stormed.
While Affleck was overlooked by the Academy for his directing role, the film has dominated other awards since the Oscar nominations, winning best director and best film at the Golden Globes and at the Critics Choice Awards.
Last weekend, Argo was victorious at both the Producers Guild and the Screen Actors Guild awards, leaving Steven Spielberg's Civil War-era epic Lincoln in its wake.
Many of the film professionals who vote in guild awards also cast ballots for the Oscars, so recognition from the DGA further seals Argo's status as best-picture front-runner at the Oscars on 24 February.
Only six times in the DGA's history has the winner failed to take the Oscar for best director.
This will be the seventh, as Affleck missed out on an Academy nomination, along with several other key favourites, including fellow Directors Guild contenders Kathryn Bigelow for Zero Dark Thirty and Tom Hooper for Les Miserables.
Backstage at the DGA ceremony on Saturday, Affleck said he had nothing but respect for the Academy, adding that "you're not entitled to anything."
"I'm thrilled and honoured that the Academy nominated me as a producer of the movie," he said.
"I know our movie, we're a little bit underdog and a little bit the little engine that could, and you take me out of it maybe helps ... it's just about that picture. I feel like it's OK, I'm really lucky, I'm in a good place."
Among the other DGA winners were Searching for Sugar Man director Malik Bendjelloul, who won the guild's documentary award for his study of the obscure singer-songwriter Sixto Rodriquez.
The film also is nominated for best documentary at the Oscars.
Lena Dunham won the TV comedy directing prize for Girls, about the lives of a group of girls in their 20s, while Rian Johnson won in the drama series series category for Breaking Bad.
Milos Forman, who directed One Flew Over the Cuckoo's Nest and Amadeus, was honoured with a lifetime-achievement award.
The 65th Annual DGA Awards, hosted by Kelsey Grammer, were held at the Ray Dolby Ballroom at Hollywood & Highland in Los Angeles.
Ben Affleck has won the top film honour from the Directors Guild of America for his Iran hostage drama, Argo.