The acquisition of Sybari will help drive Microsoft's enterprise security strategy, executives said.
"We're excited to be able to provide customers with a server-level anti-virus solution that delivers advanced file and content-filtering capabilities and the use of multiple scan engines," Mike Nash, corporate vice president of Microsoft's security business and technology unit, said in a statement.
Terms of the deal were not disclosed.
Microsoft previously acquired the anti-virus technology of GeCAD and anti-spyware firm Giant.
Symantec officials released a statement noting that Sybari does not own its core scanning technologies but has relied on third party scanning engines.
"This acquisition does not provide Microsoft with the security and anti-virus response infrastructure necessary to support the virus protection needs of enterprise customers," Symantec executives said.