"Over time, you're going to see them try to leverage this asset to get people to come over to Windows phone, which only has less than 3 percent market share," said Mark Spoonauer, editor-in-chief at Tom's Guide.
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Mojang has a loyal and largely young following, and has more than 100 million players, which will now belong to Microsoft.
"Long term, I think it could pay off if they execute," Spoonauer said.
Microsoft is primarily known for business software but this acquisition will help the company expand its gaming division, which also includes game franchises such as the "Halo" shooter game and "Forza" racing game.
—By CNBC's Christina Medici Scolaro