It took three weeks, but “Argo” finally found its way to the top of the box office.

The Warner Bros. thriller from director and star Ben Affleck, inspired by the real-life rescue of six US embassy workers during the 1979 Iranian hostage crisis, made nearly $12.4 million this weekend, according to Sunday studio estimates. “Argo” had been in second place the past two weeks and has now made about $60.8 million total.

Debuting at No. 3 was the sprawling, star-studded “Cloud Atlas,” which made a disappointing $9.4 million. The nearly three-hour drama, also from Warner Bros., was co-directed by siblings Lana and Andy Wachowski and Tom Tykwer and features an ensemble cast including Tom Hanks, Halle Berry and Hugh Grant playing multiple roles over six story lines.

Dan Fellman, head of distribution at Warner Bros., said the studio thought there might be a good chance of “Argo” coming out on top this weekend.

“We’re thrilled. An accomplishment like that is well deserved, they don’t happen very often. You would probably have to do a lot of searching to find a movie that opened in wide release to have two No. 2 weekends in a row and hit No. 1 in the third week,” Fellman said. “It’s a tribute to the film. Word-of-mouth has taken over the campaign. We have a long way to go, we have a lot of year-end accolades which will approach, and we’ll see what happens in terms of the Academy.”

On the flip side, Fellman acknowledged that “Cloud Atlas” underperformed compared to hopes that it would end up in the $11-12 million range domestically. The movie had an estimated budget of $100 million. But he pointed out that it had a higher per-screen average than any other film opening in the top 10 with $4,681.

“We did very well on the East and West coasts in a number of major cities,” he said. “We’re challenged in the Midwest and the South.”

It was a soft weekend all around, though, with several newcomers opening poorly, Hollywood.com box-office analyst Paul Dergarabedian pointed out. The horror sequel “Silent Hill: Revelation 3-D” from Open Road Films debuted at No. 5 with $8 million and the Paramount Halloween comedy “Fun Size” arrived in 10th place with just over $4 million. “Chasing Mavericks,” an inspirational surfing drama from Fox 2000, didn’t even open in the top 12 — it came in at No. 13 with $2.2 million.

The World Series might have been a factor in keeping folks away from the theaters; also, potential moviegoers along the East Coast in the path of Hurricane Sandy might have stayed home this weekend.

“The whole marketplace felt more like September than October. Back in September, we had four down weekends in a row. There was no momentum in the marketplace,” Dergarabedian said. “When a holdover is No. 1, it reflects a lack of strength in the marketplace. Every week should have a new movie topping the chart.”

As for the philosophical, centuries-spanning “Cloud Atlas,” he said: “To have a) a big budget, b) Tom Hanks and c) it’s a big, epic film, it doesn’t necessarily follow that it’s going to be a big box office hit. I admire that they went for it.”

But there’s hope on the horizon with the animated comedy “Wreck-It Ralph” coming next weekend, the latest James Bond film, “Skyfall,” opening Nov. 9 and the final installment in the “Twilight” saga due out Nov. 16. “Skyfall” opened this weekend overseas with a whopping $77.7 million in 25 countries.

“This is just one of those box office weekends we’d rather forget,” Dergarabedian said. “Unless you’re ‘Argo.’”