Terms of the deal were not disclosed.
"Atlas is a leader in campaign management and measurement for marketers and agencies. We believe this acquisition will benefit both marketers and users," Facebook's Brian Boland said in a blog post.
Atlas was part of the aQuantive group acquired by Microsoft, which ended up in a writedown and loss for Microsoft last year.
Microsoft's Dave O'Hara said the deal "will strengthen our existing partnership" with Facebook "for the benefit of both companies and their respective long-term visions."
Facebook has become the world's biggest social network with more than one billion users, but its stock has been hit by concerns about its ability to boost revenues and profitability.
The California group has been working on a number of advertising initiatives for both desktop and mobile Facebook applications.
Facebook shares rose 1.4 percent to end Thursday at $27.25.