The business, which is four years old and has five million users, operates like Facebook for communication within companies.
There had been reports the two were talking about a deal but Microsoft only confirmed the plan on Monday.
Yammer is used by firms including the motor giant Ford and the business services firm Deloitte.
Microsoft hopes the acquisition will make its range of software products more appealing.
Last year it bought the communications business Skype and is integrating it into its products, including its Office software which contributed 60% of its profits last year.
Yammer plans to continue to offer its service in the way it does currently.
Yammer’s chief executive David Sacks said: “When we started Yammer four years ago, we set out to do something big.
“We had a vision for how social networking could change the way we work. Joining Microsoft will accelerate that vision and give us access to the technologies, expertise and resources we’ll need to scale and innovate.”
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