Rob Koplowitz, a Forrester Research analyst, said Microsoft is choosing the best option for integrating Yammer into its business: Yammer is retaining a lot of independence, it will be part of the Office division and its cloud-based model will be supported.

"It's about as good a news as could have been hoped for in terms of how the deal could have been structured," Koplowitz said. "It's an acquisition, and those can always be a bit treacherous, but Microsoft is setting itself up for success."

Over time, Microsoft is likely to deepen the integration of Yammer into products like SharePoint, Office 365, Outlook and Lync, analysts said. That would continue a strategy Yammer has been pursuing for more than a year. It rolled out its first integration with SharePoint in 2010 and later enhanced it. In April this year, Yammer acquired U.K. company oneDrum, whose software lets users collaborate on Word, Excel and PowerPoint documents in real time.

However, Microsoft must also make sure Yammer continues to work well with products from other vendors, such as Salesforce.com and SAP, which it integrates with via custom connectors and using Yammer's open API (application programming interface), Koplowitz said.

"Yammer already has an aggressive integration strategy with Microsoft products, and they'll continue on with that. The concern is whether Yammer will become too focused on Microsoft integrations to the exclusion of other vendors," Koplowitz said. "Yammer has been playing Switzerland. It shouldn't now favor Microsoft and reduce the potential of a broader integration portfolio."